PeakID (cmd=annotatePeaks.pl WT_blchirp.bed mm10 -cpu 120)	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
Merged-chr1-162825988-1	chr1	162825871	162826105	+	1	NA	Intergenic	L1Md_T|LINE|L1	-13439	NM_144878	226564	Mm.155164	NM_144878	ENSMUSG00000026692	Fmo4	D1Ertd532e	flavin containing monooxygenase 4	protein-coding
Merged-chr1-174709290-1	chr1	174709116	174709465	+	1	NA	intron (NM_019445, intron 13 of 17)	L1Md_A|LINE|L1	207465	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
Merged-chr15-54799385-1	chr15	54799305	54799466	+	1	NA	Intergenic	RMER1A|Other|Other	53457	NM_010930	18133	Mm.5167	NM_010930	ENSMUSG00000037362	Nov	C130088N23Rik|CCN3	nephroblastoma overexpressed gene	protein-coding
Merged-chr2-21307802-1	chr2	21307668	21307936	+	1	NA	Intergenic	L1Md_A|LINE|L1	-59765	NM_001004761	241263	Mm.166647	NM_175706	ENSMUSG00000045967	Gpr158	5330427M13Rik|mKIAA1136	G protein-coupled receptor 158	protein-coding
Merged-chr5-137840963-1	chr5	137840845	137841082	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-4685	NM_153510	231805	Mm.379385	NM_153510	ENSMUSG00000046245	Pilra	AV021745|FDF03	paired immunoglobin-like type 2 receptor alpha	protein-coding
Merged-chr1-25667548-1	chr1	25667465	25667631	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	162159	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr15-78993129-1	chr15	78993025	78993234	+	1	NA	exon (NM_138579, exon 16 of 24)	exon (NM_138579, exon 16 of 24)	-9094	NR_105921	102465577		NR_105921	ENSMUSG00000099180	Mir6956	Gm27880|mmu-mir-6956	microRNA 6956	ncRNA
Merged-chr19-6252894-1	chr19	6252806	6252983	+	1	NA	intron (NM_194348, intron 20 of 39)	intron (NM_194348, intron 20 of 39)	11226	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
Merged-chr1-29581457-1	chr1	29581289	29581625	+	1	NA	Intergenic	L1Md_A|LINE|L1	159969	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr3-97441813-1	chr3	97441709	97441917	+	1	NA	Intergenic	L1Md_T|LINE|L1	-30634	NM_146275	258272	Mm.377406	NM_146275	ENSMUSG00000051392	Olfr1402	MOR217-1	olfactory receptor 1402	protein-coding
Merged-chr1-117165994-1	chr1	117165894	117166094	+	1	NA	Intergenic	L1Md_T|LINE|L1	1144734	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr13-53217946-1	chr13	53217867	53218026	+	1	NA	intron (NM_013846, intron 1 of 8)	intron (NM_013846, intron 1 of 8)	68163	NM_013846	26564	Mm.342774	NM_013846	ENSMUSG00000021464	Ror2	Ntrkr2	receptor tyrosine kinase-like orphan receptor 2	protein-coding
Merged-chr11-62970778-1	chr11	62970666	62970890	+	1	NA	intron (NM_025496, intron 1 of 1)	L1Md_A|LINE|L1	19585	NM_025496	66338	Mm.46166	NM_025496	ENSMUSG00000042200	Cdrt4	1700019I23Rik	CMT1A duplicated region transcript 4	protein-coding
Merged-chr1-117374312-1	chr1	117374108	117374516	+	1	NA	Intergenic	L1Md_T|LINE|L1	936416	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr15-49125053-1	chr15	49124954	49125152	+	1	NA	Intergenic	L1Md_T|LINE|L1	-333064	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
Merged-chr1-44905214-1	chr1	44905110	44905318	+	1	NA	Intergenic	L1Md_T|LINE|L1	-160265	NR_040602	75066	Mm.416932	NR_040602	ENSMUSG00000101701	4930521E06Rik	-	RIKEN cDNA 4930521E06 gene	ncRNA
Merged-chr1-9176190-1	chr1	9176093	9176287	+	1	NA	intron (NM_027671, intron 2 of 20)	L1Md_A|LINE|L1	123687	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
Merged-chr17-17034054-1	chr17	17033931	17034178	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-30049	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr13-68249998-1	chr13	68249788	68250209	+	1	NA	Intergenic	MER89|LTR|ERV1	-15267	NR_155295	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr13-66258322-1	chr13	66258157	66258488	+	1	NA	Intergenic	L1_Mur2|LINE|L1	144869	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	-	predicted gene 10324	protein-coding
Merged-chr1-33016327-1	chr1	33016231	33016423	+	1	NA	Intergenic	L1Md_T|LINE|L1	-469034	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr11-37639326-1	chr11	37639245	37639408	+	1	NA	Intergenic	L1Md_A|LINE|L1	-19663	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr15-79042716-1	chr15	79042636	79042797	+	1	NA	TTS (NM_001161712)	TTS (NM_001161712)	831	NM_015738	14429	Mm.390805	NM_015738	ENSMUSG00000114755	Galr3	Galnr3	galanin receptor 3	protein-coding
Merged-chr1-59346633-1	chr1	59346532	59346735	+	1	NA	intron (NM_001356389, intron 13 of 13)	IAPEz-int|LTR|ERVK	89727	NM_001033373	271697	Mm.297713	NM_001033373	ENSMUSG00000026023	Cdk15	Als2cr7|Pftk2	cyclin-dependent kinase 15	protein-coding
Merged-chr2-97838680-1	chr2	97838596	97838764	+	1	NA	Intergenic	L1Md_A|LINE|L1	371023	NM_178725	241568	Mm.241682	NM_178725	ENSMUSG00000050587	Lrrc4c	6430556C10Rik|NGL-1	leucine rich repeat containing 4C	protein-coding
Merged-chr10-8544966-1	chr10	8544887	8545045	+	1	NA	Intergenic	MuLV-int|LTR|ERV1	-26141	NM_177387	338362	Mm.41163	NM_177387	ENSMUSG00000047712	Ust	D930010O20Rik|UA2OST	uronyl-2-sulfotransferase	protein-coding
Merged-chr11-50325884-1	chr11	50325775	50325993	+	1	NA	promoter-TSS (NM_007597)	promoter-TSS (NM_007597)	-211	NM_001110499	12330	Mm.248827	NM_007597	ENSMUSG00000020368	Canx	1110069N15Rik|AI988026|Cnx|D11Ertd153e	calnexin	protein-coding
Merged-chr10-4914082-1	chr10	4913992	4914173	+	1	NA	intron (NM_001302531, intron 5 of 8)	L1Md_T|LINE|L1	154981	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
Merged-chr15-77612067-1	chr15	77611989	77612145	+	1	NA	Intergenic	Intergenic	-15942	NM_177820	328561	Mm.379486	NM_177820	ENSMUSG00000050014	Apol10b	9130218O11Rik	apolipoprotein L 10B	protein-coding
Merged-chr1-149298447-1	chr1	149298366	149298528	+	1	NA	Intergenic	L1Md_A|LINE|L1	623992	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr17-36194241-1	chr17	36194030	36194453	+	1	NA	Intergenic	Intergenic	-4090	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
Merged-chr1-149297496-1	chr1	149297383	149297609	+	1	NA	Intergenic	L1Md_A|LINE|L1	624943	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr10-52763390-1	chr10	52763299	52763481	+	1	NA	intron (NM_178675, intron 1 of 7)	L1Md_T|LINE|L1	72889	NM_178675	215085	Mm.338690	NM_178675	ENSMUSG00000038602	Slc35f1	Duf6|E130016L02	solute carrier family 35, member F1	protein-coding
Merged-chr1-21202036-1	chr1	21201928	21202145	+	1	NA	Intergenic	L1Md_T|LINE|L1	-16539	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
Merged-chr13-66426957-1	chr13	66426672	66427242	+	1	NA	intron (NM_183119, intron 3 of 4)	B1_Mus1|SINE|Alu	14161	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr6-136330625-1	chr6	136330424	136330826	+	1	NA	TTS (NM_001142734)	TTS (NM_001142734)	3086	NM_001142734	668137	Mm.417085	NM_001142734	ENSMUSG00000094973	Gm8994	B020013A22Rik|EG668137	predicted gene 8994	protein-coding
Merged-chrX-92802518-1	chrX	92802385	92802651	+	1	NA	Intergenic	L1Md_T|LINE|L1	-202946	NM_173783	215641	Mm.327999	NM_173783	ENSMUSG00000067649	Mageb18	B430216B18Rik	melanoma antigen family B, 18	protein-coding
Merged-chr8-21014809-1	chr8	21014719	21014900	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-10736	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr10-48233936-1	chr10	48233794	48234079	+	1	NA	Intergenic	L1Md_T|LINE|L1	1554001	NM_001358866	14806	Mm.185993	NM_010349	ENSMUSG00000056073	Grik2	AW124492|C130030K03Rik|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
Merged-chr13-66608674-1	chr13	66608576	66608773	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-167556	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr13-66521221-1	chr13	66521125	66521317	+	1	NA	Intergenic	Intergenic	-80103	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-66465108-1	chr10	66465026	66465191	+	1	NA	Intergenic	L1Md_T|LINE|L1	319812	NR_131070	77198	Mm.107617	NR_131070	ENSMUSG00000112210	4930407I19Rik	-	RIKEN cDNA 4930407I19 gene	ncRNA
Merged-chr14-111874622-1	chr14	111874512	111874732	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	199507	NM_198865	75409	Mm.235097	NM_029273	ENSMUSG00000033214	Slitrk5	2610019D03Rik	SLIT and NTRK-like family, member 5	protein-coding
Merged-chr14-19302905-1	chr14	19302798	19303012	+	1	NA	Intergenic	PB1D9|SINE|Alu	299682	NM_001024706	432825	Mm.327147	NM_001024706	ENSMUSG00000095024	Gm5458	EG432825	predicted gene 5458	protein-coding
Merged-chr13-66723864-1	chr13	66723756	66723972	+	1	NA	Intergenic	B3|SINE|B2	181486	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr11-63650120-1	chr11	63649978	63650263	+	1	NA	Intergenic	L1Md_T|LINE|L1	272164	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
Merged-chr15-79376171-1	chr15	79376092	79376250	+	1	NA	promoter-TSS (NR_035464)	promoter-TSS (NR_035464)	-871	NR_035464	100316695		NR_035464	ENSMUSG00000088901	Mir1943	mir-1943|mmu-mir-1943	microRNA 1943	ncRNA
Merged-chr10-33574936-1	chr10	33574792	33575081	+	1	NA	intron (NM_001359139, intron 2 of 4)	L1Md_A|LINE|L1	-49310	NR_152723	102632938	Mm.417656	NR_152723	ENSMUSG00000090087	Gm15939	-	predicted gene 15939	ncRNA
Merged-chr17-37636422-1	chr17	37636323	37636522	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-11789	NM_146632	258625	Mm.377599	NM_146632	ENSMUSG00000061336	Olfr116	MOR218-2	olfactory receptor 116	protein-coding
Merged-chr1-161936353-1	chr1	161936266	161936441	+	1	NA	Intergenic	L1Md_T|LINE|L1	32795	NM_001204905	75368	Mm.108728	NM_001204904	ENSMUSG00000086277	4930558K02Rik	-	RIKEN cDNA 4930558K02 gene	protein-coding
Merged-chr17-17001593-1	chr17	17001456	17001730	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-62510	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr12-64887604-1	chr12	64887446	64887763	+	1	NA	Intergenic	L1Md_A|LINE|L1	-30307	NM_001025605	217648	Mm.341586	NM_001025605	ENSMUSG00000047227	Gm527	-	predicted gene 527	protein-coding
Merged-chr1-162268095-1	chr1	162267959	162268231	+	1	NA	intron (NM_001038619, intron 13 of 20)	L1Md_A|LINE|L1	44727	NR_029796	387210		NR_029796	ENSMUSG00000065516	Mir214	Mirn214|mir-214|mmu-mir-214	microRNA 214	ncRNA
Merged-chr13-29252196-1	chr13	29252113	29252280	+	1	NA	intron (NR_131896, intron 15 of 16)	L1Md_T|LINE|L1	235941	NR_045075	77920	Mm.197051	NR_045073	ENSMUSG00000086363	A330102I10Rik	-	RIKEN cDNA A330102I10 gene	ncRNA
Merged-chr15-101438472-1	chr15	101438389	101438555	+	1	NA	exon (NM_001003668, exon 1 of 9)	exon (NM_001003668, exon 1 of 9)	332	NM_001003668	406219	Mm.347934	NM_001003668	ENSMUSG00000047641	Krt87	K83|K87|Krt2-25|Krt83	keratin 87	protein-coding
Merged-chr1-150279080-1	chr1	150278970	150279190	+	1	NA	Intergenic	L1Md_T|LINE|L1	-40337	NM_024458	20028	Mm.440883	NM_024458	ENSMUSG00000006007	Pdc	Rpr-1|Rpr1	phosducin	protein-coding
Merged-chr15-72816357-1	chr15	72816206	72816509	+	1	NA	intron (NM_001164641, intron 17 of 17)	intron (NM_001164641, intron 17 of 17)	-6033	NR_002864	353342	Mm.440245	NR_002864	ENSMUSG00000106847	Peg13	-	paternally expressed 13	ncRNA
Merged-chr1-139911633-1	chr1	139911501	139911766	+	1	NA	Intergenic	L1Md_T|LINE|L1	-52934	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
Merged-chr1-64472878-1	chr1	64472768	64472989	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-59926	NM_009952	12912	Mm.422634	NM_009952	ENSMUSG00000025958	Creb1	2310001E10Rik|3526402H21Rik|AV083133|Creb|Creb-1	cAMP responsive element binding protein 1	protein-coding
Merged-chr5-92545409-1	chr5	92545266	92545552	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-26128	NM_001170571	384198	Mm.76757	NM_001033478	ENSMUSG00000057068	Fam47e	C730043O17|Gm1381	family with sequence similarity 47, member E	protein-coding
Merged-chr19-6980273-1	chr19	6980123	6980423	+	1	NA	promoter-TSS (NM_001360288)	promoter-TSS (NM_001360288)	-187	NM_001360286	14227	Mm.4234	NM_008020	ENSMUSG00000056629	Fkbp2	mFKBP13|mFKBP2	FK506 binding protein 2	protein-coding
Merged-chr1-116862105-1	chr1	116862025	116862186	+	1	NA	Intergenic	L1Md_T|LINE|L1	1176968	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr1-158644898-1	chr1	158644667	158645129	+	1	NA	intron (NM_007495, intron 16 of 22)	L1Md_T|LINE|L1	139273	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
Merged-chr13-66296177-1	chr13	66295939	66296415	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	144941	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-100231053-1	chr1	100230936	100231170	+	1	NA	intron (NM_172851, intron 11 of 23)	IAPEY4_I-int|LTR|ERVK	458288	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr19-41503112-1	chr19	41503031	41503193	+	1	NA	Intergenic	B3|SINE|B2	-22140	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
Merged-chr12-47579779-1	chr12	47579676	47579883	+	1	NA	Intergenic	L1Md_T|LINE|L1	-761004	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
Merged-chr13-68356763-1	chr13	68356634	68356893	+	1	NA	promoter-TSS (NR_152173)	promoter-TSS (NR_152173)	62	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr18-20621562-1	chr18	20621481	20621643	+	1	NA	intron (NR_155534, intron 1 of 2)	L1M3e|LINE|L1	-43688	NM_013697	22139	Mm.2108	NM_013697	ENSMUSG00000061808	Ttr	AA408768|AI787086|D17860|prealbumin	transthyretin	protein-coding
Merged-chr17-27388557-1	chr17	27388477	27388638	+	1	NA	Intergenic	ORR1D1|LTR|ERVL-MaLR	30460	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr1-83246294-1	chr1	83246148	83246440	+	1	NA	Intergenic	L1Md_T|LINE|L1	86532	NR_027636	71227	Mm.256482	NM_027725	ENSMUSG00000053161	Daw1	4930563E19Rik|4933429D11Rik|Wdr69|b2b1116Clo|b2b1584Clo	dynein assembly factor with WDR repeat domains 1	protein-coding
Merged-chr5-87542702-1	chr5	87542596	87542808	+	1	NA	Intergenic	L1Md_T|LINE|L1	-4507	NM_019878	56362	Mm.23502	NM_019878	ENSMUSG00000029269	Sult1b1	ST1B1|St2b2	sulfotransferase family 1B, member 1	protein-coding
Merged-chr12-94849882-1	chr12	94849772	94849992	+	1	NA	Intergenic	L1Md_T|LINE|L1	-842344	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
Merged-chr1-98115899-1	chr1	98115773	98116026	+	1	NA	Intergenic	L1Md_A|LINE|L1	-15568	NR_040439	69030	Mm.402692	NR_040439	ENSMUSG00000100182	1810006J02Rik	-	RIKEN cDNA 1810006J02 gene	ncRNA
Merged-chr10-69233584-1	chr10	69233443	69233725	+	1	NA	intron (NM_001252638, intron 2 of 11)	L1Md_T|LINE|L1	20390	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
Merged-chr10-80172408-1	chr10	80172325	80172491	+	1	NA	promoter-TSS (NM_027207)	promoter-TSS (NM_027207)	-536	NM_027207	69770	Mm.302754	NM_027207	ENSMUSG00000035595	1600002K03Rik	-	RIKEN cDNA 1600002K03 gene	protein-coding
Merged-chr1-50335995-1	chr1	50335903	50336088	+	1	NA	Intergenic	L1Md_T|LINE|L1	-591528	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
Merged-chr15-101073006-1	chr15	101072907	101073105	+	1	NA	Intergenic	Intergenic	-18607	NM_001214911	668225	Mm.385011	NM_001214911	ENSMUSG00000095440	Fignl2	EG668225	fidgetin-like 2	protein-coding
Merged-chr17-21149049-1	chr17	21148942	21149156	+	1	NA	Intergenic	Intergenic	57841	NR_137274	328766	Mm.50947	NR_137274	ENSMUSG00000102080	Gm5092	4933430A09	predicted gene 5092	ncRNA
Merged-chr15-95776037-1	chr15	95775938	95776136	+	1	NA	Intergenic	Intergenic	-14806	NM_001253813	105722	Mm.38087	NM_175344	ENSMUSG00000064210	Ano6	2900059G15Rik|AA407480|AW554778|F730003B03Rik|Tmem16f	anoctamin 6	protein-coding
Merged-chr12-37191322-1	chr12	37191213	37191431	+	1	NA	Intergenic	L1Md_T|LINE|L1	-50317	NM_178767	319660	Mm.485540	NM_178767	ENSMUSG00000050103	Agmo	A530016O06Rik|AI790538|Tmem195	alkylglycerol monooxygenase	protein-coding
Merged-chr13-62434762-1	chr13	62434644	62434881	+	1	NA	Intergenic	Intergenic	32050	NM_001136496	71508	Mm.442497	NM_178875	ENSMUSG00000113450	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
Merged-chr13-66822985-1	chr13	66822900	66823071	+	1	NA	Intergenic	RLTR1A2_MM|LTR|ERV1	82365	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr10-80533075-1	chr10	80532961	80533190	+	1	NA	intron (NM_026094, intron 8 of 27)	intron (NM_026094, intron 8 of 27)	6049	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
Merged-chr13-66717945-1	chr13	66717859	66718032	+	1	NA	Intergenic	L1_Mus2|LINE|L1	187405	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr13-66284868-1	chr13	66284651	66285085	+	1	NA	Intergenic	B3|SINE|B2	156250	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-74417473-1	chr15	74417363	74417583	+	1	NA	intron (NR_144499, intron 3 of 3)	intron (NR_144499, intron 3 of 3)	70173	NR_144499	102634630		NR_144499		Gm32168	-	predicted gene, 32168	ncRNA
Merged-chr4-62510959-1	chr4	62510713	62511206	+	1	NA	intron (NM_001276446, intron 7 of 11)	intron (NM_001276446, intron 7 of 11)	-8759	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
Merged-chr15-74776386-1	chr15	74776304	74776468	+	1	NA	intron (NR_027836, intron 1 of 2)	(TGGA)n|Simple_repeat|Simple_repeat	2473	NR_027837	78725	Mm.171357	NM_172433	ENSMUSG00000101026	D730001G18Rik	Ly6g6g	RIKEN cDNA D730001G18 gene	ncRNA
Merged-chr13-36978759-1	chr13	36978636	36978882	+	1	NA	intron (NM_001166391, intron 4 of 14)	GA-rich|Low_complexity|Low_complexity	70454	NM_028784	74145	Mm.235105	NM_028784	ENSMUSG00000039109	F13a1	1200014I03Rik|AI462306|F13a	coagulation factor XIII, A1 subunit	protein-coding
Merged-chr15-73028961-1	chr15	73028816	73029106	+	1	NA	intron (NM_029640, intron 5 of 21)	intron (NM_029640, intron 5 of 21)	26851	NM_029640	76510	Mm.158902	NM_029640	ENSMUSG00000047921	Trappc9	1810044A24Rik|2900005P22Rik|4632408O18Rik|Ibp|Nibp|TRS130|mKIAA1882	trafficking protein particle complex 9	protein-coding
Merged-chr2-157396079-1	chr2	157395991	157396168	+	1	NA	3' UTR (NM_026968, exon 3 of 3)	3' UTR (NM_026968, exon 3 of 3)	-28214	NM_001025395	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
Merged-chr11-37756829-1	chr11	37756564	37757094	+	1	NA	Intergenic	L1Md_T|LINE|L1	97840	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr10-52498326-1	chr10	52498140	52498513	+	1	NA	Intergenic	L1Md_T|LINE|L1	47413	NR_037920	22639	Mm.490597	NM_009540	ENSMUSG00000049576	Zfa-ps	Zfa|Zfx	zinc finger protein, autosomal, pseudogene	pseudo
Merged-chr17-38514758-1	chr17	38514625	38514891	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-39434	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-30039429-1	chr1	30039320	30039538	+	1	NA	Intergenic	L1Md_A|LINE|L1	617941	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr3-102906112-1	chr3	102906003	102906221	+	1	NA	intron (NM_011516, intron 16 of 32)	MTA_Mm|LTR|ERVL-MaLR	29988	NM_011516	20957	Mm.243849	NM_011516	ENSMUSG00000027855	Sycp1	SCP1	synaptonemal complex protein 1	protein-coding
Merged-chr2-144156138-1	chr2	144155999	144156278	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	33152	NR_136884	433481	Mm.330630	NR_136884	ENSMUSG00000074758	Gm5535	EG433481	predicted gene 5535	ncRNA
Merged-chr13-81586133-1	chr13	81586002	81586264	+	1	NA	intron (NM_054053, intron 4 of 89)	L1Md_T|LINE|L1	47011	NM_054053	110789	Mm.288694	NM_054053	ENSMUSG00000069170	Adgrv1	Frings|Gpr98|Mass1|Mgr1|VLGR1	adhesion G protein-coupled receptor V1	protein-coding
Merged-chr13-62187441-1	chr13	62187360	62187522	+	1	NA	Intergenic	Lx3A|LINE|L1	57551	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr14-123880508-1	chr14	123880429	123880587	+	1	NA	intron (NM_145467, intron 7 of 10)	L1Md_A|LINE|L1	-107127	NR_045479	69393	Mm.491348	NR_045479	ENSMUSG00000099994	1700024B18Rik	-	RIKEN cDNA 1700024B18 gene	ncRNA
Merged-chr1-11780526-1	chr1	11780436	11780617	+	1	NA	intron (NM_001160369, intron 8 of 13)	L1Md_T|LINE|L1	366421	NM_001160370	320492	Mm.52021	NM_177173	ENSMUSG00000057715	A830018L16Rik	-	RIKEN cDNA A830018L16 gene	protein-coding
Merged-chr18-89917376-1	chr18	89917294	89917458	+	1	NA	Intergenic	L1Md_A|LINE|L1	-148240	NM_001039173	623279	Mm.447164	NM_001039173	ENSMUSG00000073514	Dok6	Dok-6	docking protein 6	protein-coding
Merged-chr13-16603098-1	chr13	16603004	16603193	+	1	NA	Intergenic	L1Md_T|LINE|L1	-579675	NR_155430	100503142	Mm.359204	NR_155430		B230303A05Rik	B230303A05|EG328191	U1 small nuclear ribonucleoprotein 1C pseudogene	pseudo
Merged-chr1-50330759-1	chr1	50330633	50330885	+	1	NA	Intergenic	L1Md_T|LINE|L1	-596764	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
Merged-chr13-106379885-1	chr13	106379791	106379979	+	1	NA	Intergenic	L1Md_A|LINE|L1	557073	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
Merged-chr17-72575890-1	chr17	72575594	72576187	+	1	NA	intron (NM_007439, intron 1 of 28)	IAPEz-int|LTR|ERVK	28417	NM_007439	11682	Mm.311854	NM_007439	ENSMUSG00000055471	Alk	CD246|Tcrz	anaplastic lymphoma kinase	protein-coding
Merged-chr12-49055068-1	chr12	49054986	49055150	+	1	NA	Intergenic	L1Md_T|LINE|L1	-327815	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
Merged-chr10-71819774-1	chr10	71819545	71820004	+	1	NA	Intergenic	L1Md_A|LINE|L1	160916	NR_003644	108950	Mm.212793	NM_175390		1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
Merged-chr1-163784691-1	chr1	163784611	163784772	+	1	NA	intron (NM_001305643, intron 2 of 19)	L1Md_T|LINE|L1	5108	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
Merged-chr1-138454548-1	chr1	138454435	138454661	+	1	NA	Intergenic	L1Md_A|LINE|L1	165209	NM_001311148	59125	Mm.143817	NM_021605	ENSMUSG00000026393	Nek7	2810460C19Rik|AU020186	NIMA (never in mitosis gene a)-related expressed kinase 7	protein-coding
Merged-chr13-67968076-1	chr13	67967992	67968160	+	1	NA	Intergenic	Intergenic	104750	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr10-41315385-1	chr10	41315295	41315475	+	1	NA	Intergenic	L1Md_T|LINE|L1	-12144	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
Merged-chr12-115602045-1	chr12	115601898	115602192	+	1	NA	Intergenic	Lx7|LINE|L1	93749	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr15-38938704-1	chr15	38938554	38938854	+	1	NA	intron (NM_080640, intron 1 of 1)	intron (NM_080640, intron 1 of 1)	4795	NM_080640	118452	Mm.233837	NM_080640	ENSMUSG00000022296	Baalc	2810457D07Rik	brain and acute leukemia, cytoplasmic	protein-coding
Merged-chr19-6071093-1	chr19	6071003	6071184	+	1	NA	exon (NM_001081041, exon 5 of 10)	exon (NM_001081041, exon 5 of 10)	-3243	NM_028454	73166	Mm.489613	NM_028454	ENSMUSG00000024799	Tm7sf2	3110041O18Rik|ANG1|C14SR|Dhcr14	transmembrane 7 superfamily member 2	protein-coding
Merged-chr15-74716370-1	chr15	74716192	74716548	+	1	NA	intron (NM_028216, intron 2 of 2)	intron (NM_028216, intron 2 of 2)	1531	NM_028216	72373	Mm.46395	NM_028216	ENSMUSG00000022598	Psca	2210408B04Rik	prostate stem cell antigen	protein-coding
Merged-chr10-17148010-1	chr10	17147831	17148189	+	1	NA	Intergenic	L1Md_T|LINE|L1	-52228	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chrX-3218784-1	chrX	3218675	3218894	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	141864	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr1-83674871-1	chr1	83674752	83674991	+	1	NA	Intergenic	L1Md_A|LINE|L1	-266671	NM_001356547	77629	Mm.154303	NM_172430	ENSMUSG00000026163	Sphkap	4930544G21Rik|A930009L15Rik|AI852220|SKIP|mKIAA1678	SPHK1 interactor, AKAP domain containing	protein-coding
Merged-chr10-35355992-1	chr10	35355873	35356112	+	1	NA	Intergenic	L1Md_A|LINE|L1	872592	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
Merged-chr13-64832496-1	chr13	64832406	64832587	+	1	NA	intron (NM_001081129, intron 3 of 23)	MuRRS-int|LTR|ERV1	71392	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding
Merged-chr2-157457799-1	chr2	157457678	157457920	+	1	NA	intron (NM_001025395, intron 4 of 13)	intron (NM_001025395, intron 4 of 13)	33506	NM_009271	20779	Mm.22845	NM_009271	ENSMUSG00000027646	Src	AW259666|pp60c-src	Rous sarcoma oncogene	protein-coding
Merged-chr10-5395198-1	chr10	5395027	5395370	+	1	NA	intron (NM_001347711, intron 13 of 145)	L1Md_A|LINE|L1	93116	NM_001347711	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
Merged-chr12-43729408-1	chr12	43729320	43729496	+	1	NA	Intergenic	L1Md_T|LINE|L1	480660	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
Merged-chr11-115047570-1	chr11	115047463	115047677	+	1	NA	intron (NM_199201, intron 1 of 3).2	intron (NM_199201, intron 1 of 3).2	725	NM_199201	382551	Mm.424732	NM_199201	ENSMUSG00000069607	Cd300ld3	AY457049|Cd300lh|Clm3|Lmir7|clm-3	CD300 molecule like family member D3	protein-coding
Merged-chr15-97832237-1	chr15	97832109	97832366	+	1	NA	promoter-TSS (NM_001204276)	promoter-TSS (NM_001204276)	-470	NM_001204277	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
Merged-chr15-101239028-1	chr15	101238942	101239115	+	1	NA	Intergenic	Intergenic	-13842	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
Merged-chr1-73647340-1	chr1	73647246	73647435	+	1	NA	intron (NR_045311, intron 7 of 8)	L1Md_A|LINE|L1	208235	NR_105769	102465179		NR_105769	ENSMUSG00000098504	Mir6351	Gm27936|mmu-mir-6351	microRNA 6351	ncRNA
Merged-chr13-100420174-1	chr13	100420068	100420281	+	1	NA	intron (NM_008670, intron 12 of 15)	RLTR10C|LTR|ERVK	32690	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
Merged-chr17-33190578-1	chr17	33190493	33190664	+	1	NA	Intergenic	Intergenic	-8484	NM_207175	100038860	Mm.377394	NM_207175	ENSMUSG00000093884	Olfr239	MOR267-10	olfactory receptor 239	protein-coding
Merged-chr1-43852000-1	chr1	43851848	43852152	+	1	NA	Intergenic	L1Md_A|LINE|L1	-24292	NM_026430	67883	Mm.387202	NM_026430	ENSMUSG00000057363	Uxs1	1600025I13Rik|AI451869|AI649125|AW550562	UDP-glucuronate decarboxylase 1	protein-coding
Merged-chr13-74356853-1	chr13	74356753	74356953	+	1	NA	exon (NM_001168659, exon 3 of 3)	exon (NM_001168659, exon 3 of 3)	6536	NM_001168659	67433	Mm.101586	NM_024201	ENSMUSG00000021578	Ccdc127	0610011N22Rik|5430420E17Rik|A430066A18|AI256405|AW050060|C130002N06	coiled-coil domain containing 127	protein-coding
Merged-chr11-42780032-1	chr11	42779930	42780135	+	1	NA	Intergenic	L1Md_T|LINE|L1	358682	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
Merged-chr13-66395089-1	chr13	66394955	66395224	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	46029	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-76205681-1	chr15	76205541	76205822	+	1	NA	exon (NM_001163540, exon 1 of 33)	exon (NM_001163540, exon 1 of 33)	640	NM_001163540	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr17-34767950-1	chr17	34767828	34768073	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-24053	NM_009780	12268	Mm.477109	NM_009780	ENSMUSG00000073418	C4b	C4|Ss	complement component 4B (Chido blood group)	protein-coding
Merged-chr12-115504376-1	chr12	115504285	115504468	+	1	NA	Intergenic	Intergenic	191418	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr10-73439098-1	chr10	73439016	73439181	+	1	NA	Intergenic	L1Md_T|LINE|L1	-352393	NR_040646	327768	Mm.417745	NR_040646	ENSMUSG00000111994	A330049N07Rik	-	RIKEN cDNA A330049N07 gene	ncRNA
Merged-chr4-52190541-1	chr4	52190441	52190642	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-139431	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
Merged-chr1-72543390-1	chr1	72543254	72543526	+	1	NA	Intergenic	L1Md_A|LINE|L1	-6826	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
Merged-chr1-101760735-1	chr1	101760649	101760822	+	1	NA	Intergenic	L1Md_T|LINE|L1	604967	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr10-102427628-1	chr10	102427387	102427869	+	1	NA	Intergenic	L1Md_T|LINE|L1	53191	NM_026243	67569	Mm.25252	NM_026243	ENSMUSG00000019888	Mgat4c	9130411I17Rik|GntIVh	MGAT4 family, member C	protein-coding
Merged-chr1-130109871-1	chr1	130109791	130109952	+	1	NA	intron (NM_172485, intron 16 of 27)	L1Md_F2|LINE|L1	-312953	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr1-175341524-1	chr1	175341437	175341612	+	1	NA	intron (NM_001199003, intron 2 of 17)	L1Md_T|LINE|L1	151021	NM_001347195	24012	Mm.7956	NM_011880	ENSMUSG00000026527	Rgs7	-	regulator of G protein signaling 7	protein-coding
Merged-chr9-122742145-1	chr9	122742055	122742235	+	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	-5201	NM_001199736	671232	Mm.296421	NM_001199736	ENSMUSG00000094985	Topaz1	Gm9524	testis and ovary specific PAZ domain containing 1	protein-coding
Merged-chr8-72037805-1	chr8	72037715	72037895	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-19855	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr3-155149440-1	chr3	155149328	155149553	+	1	NA	intron (NM_028938, intron 5 of 7)	L1Md_T|LINE|L1	56006	NM_028938	74435	Mm.195711	NM_028938	ENSMUSG00000028182	Lrriq3	4930438B07Rik|4930511J15Rik|4933403H06Rik|BB020367|Lrrc44	leucine-rich repeats and IQ motif containing 3	protein-coding
Merged-chr1-20435304-1	chr1	20435145	20435463	+	1	NA	intron (NM_153179, intron 36 of 66)	L1Md_T|LINE|L1	78850	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chr5-145760852-1	chr5	145760635	145761069	+	1	NA	Intergenic	RLTR10D|LTR|ERVK	-40716	NM_017396	53973	Mm.379071	NM_017396	ENSMUSG00000075551	Cyp3a41a	Cyp3a41	cytochrome P450, family 3, subfamily a, polypeptide 41A	protein-coding
Merged-chr1-106080230-1	chr1	106080144	106080317	+	1	NA	Intergenic	L1Md_F2|LINE|L1	89824	NM_001122675	227449	Mm.210188	NM_001122675	ENSMUSG00000038866	Zcchc2	9930114B20Rik|AW212015	zinc finger, CCHC domain containing 2	protein-coding
Merged-chr13-68074661-1	chr13	68074529	68074794	+	1	NA	Intergenic	Lx2|LINE|L1	157159	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr4-132990634-1	chr4	132990551	132990717	+	1	NA	intron (NM_010208, intron 5 of 12)	intron (NM_010208, intron 5 of 12)	16539	NM_010208	14191	Mm.271665	NM_010208	ENSMUSG00000028874	Fgr	-	FGR proto-oncogene, Src family tyrosine kinase	protein-coding
Merged-chr5-146478625-1	chr5	146478458	146478792	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-3318	NM_001243104	623198	Mm.489582	NM_001243104	ENSMUSG00000096344	Gm6408	-	predicted gene 6408	protein-coding
Merged-chr12-91940531-1	chr12	91940381	91940681	+	1	NA	Intergenic	L1Md_T|LINE|L1	-91374	NM_011344	20338	Mm.250605	NM_011344	ENSMUSG00000020964	Sel1l	AW493766|Sel1h|mKIAA4137	sel-1 suppressor of lin-12-like (C. elegans)	protein-coding
Merged-chr17-26455452-1	chr17	26455338	26455567	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	40487	NM_001081656	240055	Mm.133211	NM_001081656	ENSMUSG00000034413	Neurl1b	C230078M08Rik|EG240055	neuralized E3 ubiquitin protein ligase 1B	protein-coding
Merged-chr5-146502676-1	chr5	146502456	146502897	+	1	NA	intron (NM_026136, intron 1 of 4)	intron (NM_026136, intron 1 of 4)	277	NM_026136	67410	Mm.463005	NM_026136	ENSMUSG00000079093	4930449I24Rik	-	RIKEN cDNA 4930449I24 gene	protein-coding
Merged-chr5-23298206-1	chr5	23298102	23298310	+	1	NA	Intergenic	L1Md_F2|LINE|L1	136147	NR_040469	269630	Mm.425231	NR_040469	ENSMUSG00000073147	5031425E22Rik	-	RIKEN cDNA 5031425E22 gene	ncRNA
Merged-chr15-58823725-1	chr15	58823621	58823830	+	1	NA	promoter-TSS (NM_175212)	promoter-TSS (NM_175212)	-298	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
Merged-chr7-38177303-1	chr7	38177184	38177423	+	1	NA	Intergenic	MLTR25A|LTR|ERVK	-5914	NM_001085385	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
Merged-chr15-4066869-1	chr15	4066768	4066970	+	1	NA	intron (NM_024188, intron 7 of 16)	Lx2|LINE|L1	-39463	NR_028266	414066	Mm.394461	NR_028266		BC037032	-	cDNA Sequence BC037032	ncRNA
Merged-chr19-41982061-1	chr19	41981811	41982312	+	1	NA	promoter-TSS (NM_028152)	promoter-TSS (NM_028152)	298	NM_145500	226122	Mm.22948	NM_145500	ENSMUSG00000025171	Ubtd1	BC016129	ubiquitin domain containing 1	protein-coding
Merged-chr19-5654293-1	chr19	5654209	5654378	+	1	NA	intron (NM_001164481, intron 10 of 17)	CpG-7241	9414	NM_011379	20469	Mm.3072	NM_011379	ENSMUSG00000056917	Sipa1	Spa1	signal-induced proliferation associated gene 1	protein-coding
Merged-chr12-37780102-1	chr12	37780017	37780187	+	1	NA	Intergenic	L1Md_A|LINE|L1	-100072	NM_001361688	217480	Mm.126525	NM_178681	ENSMUSG00000036095	Dgkb	6430574F24|90kda|C630029D13Rik|DAGK2|DGK|DGK-beta|mKIAA0718	diacylglycerol kinase, beta	protein-coding
Merged-chr12-90962747-1	chr12	90962581	90962914	+	1	NA	Intergenic	L1Md_T|LINE|L1	-83101	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
Merged-chr10-55485125-1	chr10	55485009	55485241	+	1	NA	Intergenic	L1Md_T|LINE|L1	-621792	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr19-8173926-1	chr19	8173848	8174005	+	1	NA	intron (NM_172776, intron 5 of 9)	L1Md_F2|LINE|L1	-41944	NM_001013820	434674	Mm.24053	NM_001013820	ENSMUSG00000063590	Slc22a28	EG434674|Gm5631	solute carrier family 22, member 28	protein-coding
Merged-chr11-75671722-1	chr11	75671191	75672254	+	1	NA	exon (NM_008659, exon 28 of 32)	exon (NM_008659, exon 28 of 32)	-7537	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
Merged-chr11-28350694-1	chr11	28350464	28350924	+	1	NA	Intergenic	L1Md_T|LINE|L1	233630	NM_001346759	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
Merged-chr4-132422173-1	chr4	132422071	132422276	+	1	NA	intron (NM_001161797, intron 1 of 12)	CpG	273	NM_001161797	100169	Mm.158361	NM_175306	ENSMUSG00000066043	Phactr4	3110001B12Rik|AI527228|AW495572|C330013F19Rik|N28169|mKIAA4120	phosphatase and actin regulator 4	protein-coding
Merged-chr5-47970140-1	chr5	47970013	47970268	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-13015	NM_001291228	20563	Mm.289739	NM_178804	ENSMUSG00000031558	Slit2	Drad-1|E030015M03Rik|E130320P19Rik|Slil3|b2b1200.1Clo|mKIAA4141|slit-2	slit guidance ligand 2	protein-coding
Merged-chr15-80296811-1	chr15	80296673	80296950	+	1	NA	intron (NM_001044308, intron 1 of 36)	intron (NM_001044308, intron 1 of 36)	9573	NM_001044308	239556	Mm.291058	NM_001044308	ENSMUSG00000022416	Cacna1i	Ca(V)3.3	calcium channel, voltage-dependent, alpha 1I subunit	protein-coding
Merged-chr17-26953327-1	chr17	26953237	26953417	+	1	NA	intron (NM_001281491, intron 5 of 18)	intron (NM_001281491, intron 5 of 18)	-5208	NR_037244	100526534		NR_037244	ENSMUSG00000093118	Mir3083	mir-3083|mmu-mir-3083	microRNA 3083	ncRNA
Merged-chr7-9970757-1	chr7	9970676	9970839	+	1	NA	Intergenic	G-rich|Low_complexity|Low_complexity	-17172	NM_001105152	625580	Mm.469893	NM_001105152	ENSMUSG00000095914	Vmn2r48	EG625580	vomeronasal 2, receptor 48	protein-coding
Merged-chr15-96655792-1	chr15	96655679	96655905	+	1	NA	Intergenic	Intergenic	-12879	NM_001166458	105727	Mm.103568	NM_134086	ENSMUSG00000023169	Slc38a1	AA408026|AA409865|AL022800|AU015942|NAT2	solute carrier family 38, member 1	protein-coding
Merged-chr17-46846272-1	chr17	46846144	46846401	+	1	NA	Intergenic	Intergenic	-14859	NM_001100452	210982	Mm.37642	NM_001100452	ENSMUSG00000036568	Bicral	Gltscr1l|mKIAA0240	BRD4 interacting chromatin remodeling complex associated protein like	protein-coding
Merged-chr17-17017604-1	chr17	17017506	17017702	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-46499	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr17-27547532-1	chr17	27547453	27547612	+	1	NA	Intergenic	Intergenic	-9042	NM_001166542	15361	Mm.4438	NM_016660	ENSMUSG00000046711	Hmga1	AL023995|Hmga1a|Hmga1b|Hmgi|Hmgiy|Hmgy	high mobility group AT-hook 1	protein-coding
Merged-chr14-123731285-1	chr14	123731192	123731378	+	1	NA	intron (NM_145467, intron 2 of 10)	L1Md_T|LINE|L1	71145	NM_145467	223272	Mm.383176	NM_145467	ENSMUSG00000032925	Itgbl1	B930011D01Rik	integrin, beta-like 1	protein-coding
Merged-chr17-27115041-1	chr17	27114957	27115125	+	1	NA	exon (NM_080553, exon 45 of 58)	exon (NM_080553, exon 45 of 58)	18850	NM_026063	67267	Mm.272389	NM_026063	ENSMUSG00000024208	Uqcc2	2900010M23Rik|Cbp6|M19|Mnf1	ubiquinol-cytochrome c reductase complex assembly factor 2	protein-coding
Merged-chr6-120133651-1	chr6	120133558	120133744	+	1	NA	intron (NM_016718, intron 1 of 3)	IAPEz-int|LTR|ERVK	40271	NM_016718	29862	Mm.103668	NM_016718	ENSMUSG00000041377	Ninj2	-	ninjurin 2	protein-coding
Merged-chr13-23408292-1	chr13	23407929	23408656	+	1	NA	Intergenic	Intergenic	15574	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
Merged-chr11-38905021-1	chr11	38904872	38905171	+	1	NA	Intergenic	L1Md_A|LINE|L1	-384976	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	-	predicted gene 12130	ncRNA
Merged-chr13-66739450-1	chr13	66739352	66739549	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	165900	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr17-40697258-1	chr17	40697157	40697359	+	1	NA	Intergenic	L1Md_A|LINE|L1	-29862	NM_001038500	619517	Mm.391018	NM_001038500	ENSMUSG00000073396	Esp1	EG619517|Gm6084	exocrine gland secreted peptide 1	protein-coding
Merged-chr15-38301435-1	chr15	38301353	38301518	+	1	NA	promoter-TSS (NM_001289471)	promoter-TSS (NM_001289471)	-724	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
Merged-chr3-22515574-1	chr3	22515475	22515674	+	1	NA	Intergenic	L1Md_A|LINE|L1	264204	NR_004439	19784		NR_004439		Rprl2	RPRH3|Rmrp3	ribonuclease P RNA-like 2	ncRNA
Merged-chr13-66430453-1	chr13	66430300	66430607	+	1	NA	TTS (NM_001290196)	TTS (NM_001290196)	10665	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr17-35302254-1	chr17	35302168	35302341	+	1	NA	Intergenic	Intergenic	-18293	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
Merged-chr19-41501881-1	chr19	41501721	41502042	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-23371	NM_001326287	627352	Mm.395111	NM_001326287		Morf4l1b	EG627352|Gm6747	mortality factor 4 like 1B	protein-coding
Merged-chr15-78918139-1	chr15	78918045	78918233	+	1	NA	exon (NM_020271, exon 2 of 2)	exon (NM_020271, exon 2 of 2)	4220	NM_020271	57028	Mm.263169	NM_020271	ENSMUSG00000116165	Pdxp	1600027H05Rik|AB041662|PLPP	pyridoxal (pyridoxine, vitamin B6) phosphatase	protein-coding
Merged-chr5-115272639-1	chr5	115272561	115272717	+	1	NA	5' UTR (NM_016698, exon 1 of 17)	5' UTR (NM_016698, exon 1 of 17)	256	NM_001302449	50849	Mm.30051	NM_016698	ENSMUSG00000041740	Rnf10	AA675014|RIE2|mKIAA0262	ring finger protein 10	protein-coding
Merged-chr1-166469912-1	chr1	166469827	166469997	+	1	NA	Intergenic	L1Md_T|LINE|L1	-14424	NR_151518	102636226	Mm.412602	NR_151518		Gm33354	-	predicted gene, 33354	ncRNA
Merged-chr19-7507775-1	chr19	7507690	7507861	+	1	NA	intron (NM_146091, intron 1 of 12)	ORR1B1|LTR|ERVL-MaLR	13337	NM_146091	109168	Mm.264016	NM_146091	ENSMUSG00000024759	Atl3	4633402C03Rik|5730596K20Rik|AI465397|AW228836	atlastin GTPase 3	protein-coding
Merged-chr15-75712275-1	chr15	75712170	75712381	+	1	NA	exon (NM_008164, exon 11 of 15)	exon (NM_008164, exon 11 of 15)	7987	NM_001163465	14787	Mm.57052	NM_008164	ENSMUSG00000022580	Rhpn1	BB023497|Grbp|Rhophilin|mKIAA1929	rhophilin, Rho GTPase binding protein 1	protein-coding
Merged-chr19-29692653-1	chr19	29692459	29692848	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-5288	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
Merged-chr15-96451670-1	chr15	96451580	96451761	+	1	NA	intron (NM_028148, intron 1 of 14)	intron (NM_028148, intron 1 of 14)	9173	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
Merged-chr13-22908113-1	chr13	22907947	22908279	+	1	NA	Intergenic	L1Md_A|LINE|L1	-23952	NM_134241	171275	Mm.377227	NM_134241	ENSMUSG00000071490	Vmn1r212	V1rh18	vomeronasal 1 receptor 212	protein-coding
Merged-chrX-157259236-1	chrX	157259116	157259356	+	1	NA	intron (NM_011077, intron 13 of 21)	(TAGA)n|Simple_repeat|Simple_repeat	156050	NM_011077	18675	Mm.2529	NM_011077	ENSMUSG00000057457	Phex	Gy|HPDR|HPDR1|Hyp|PEX	phosphate regulating endopeptidase homolog, X-linked	protein-coding
Merged-chr17-24573430-1	chr17	24573349	24573511	+	1	NA	exon (NM_013630, exon 15 of 46)	exon (NM_013630, exon 15 of 46)	23480	NM_013630	18763	Mm.30435	NM_013630	ENSMUSG00000032855	Pkd1	PC1|mFLJ00285	polycystin 1, transient receptor poteintial channel interacting	protein-coding
Merged-chr1-121162152-1	chr1	121161996	121162308	+	1	NA	Intergenic	L1Md_A|LINE|L1	74747	NR_110450	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
Merged-chr1-107828240-1	chr1	107828111	107828369	+	1	NA	Intergenic	L1Md_T|LINE|L1	-89019	NR_102307	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr8-21654721-1	chr8	21654555	21654888	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-1046	NM_001167790	23855	Mm.425519	NM_001167790	ENSMUSG00000060208	Defa17	AU014719|Cryp17|Defcr17	defensin, alpha, 17	protein-coding
Merged-chr15-8725609-1	chr15	8725479	8725740	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-14802	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
Merged-chr13-68318825-1	chr13	68318694	68318957	+	1	NA	Intergenic	Intergenic	38000	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr5-23728285-1	chr5	23728164	23728407	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-15618	NR_038090	433855	Mm.205125	NR_015554	ENSMUSG00000105987	AI506816	-	expressed sequence AI506816	ncRNA
Merged-chr3-144655184-1	chr3	144655092	144655277	+	1	NA	Intergenic	L1Md_T|LINE|L1	65151	NM_001282037	54673	Mm.271775	NM_019464	ENSMUSG00000037062	Sh3glb1	AA409932|AI314629|AU015566|Bif-1|mKIAA0491	SH3-domain GRB2-like B1 (endophilin)	protein-coding
Merged-chr12-82636968-1	chr12	82636762	82637175	+	1	NA	intron (NM_001282061, intron 1 of 16)	L1Md_T|LINE|L1	19469	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
Merged-chr1-104276440-1	chr1	104276337	104276543	+	1	NA	Intergenic	L1Md_T|LINE|L1	-492080	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr13-66439186-1	chr13	66439092	66439280	+	1	NA	intron (NM_001290196, intron 1 of 3)	intron (NM_001290196, intron 1 of 3)	1932	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-77765703-1	chr15	77765600	77765806	+	1	NA	exon (NM_022410, exon 35 of 41)	exon (NM_022410, exon 35 of 41)	-8693	NM_001357895	239552	Mm.125650	NM_001081970	ENSMUSG00000056656	Apol8	9830006J20Rik|APOL-II|Apol2	apolipoprotein L 8	protein-coding
Merged-chr15-83555448-1	chr15	83555211	83555686	+	1	NA	exon (NM_001030014, exon 1 of 4)	exon (NM_001030014, exon 1 of 4)	263	NM_001030014	223722	Mm.37560	NM_001030014	ENSMUSG00000048755	Mcat	AI225907|BC025519	malonyl CoA:ACP acyltransferase (mitochondrial)	protein-coding
Merged-chr17-34472547-1	chr17	34472440	34472655	+	1	NA	intron (NM_030746, intron 4 of 8)	intron (NM_030746, intron 4 of 8)	3390	NM_030746	632126	Mm.484958	NM_030746	ENSMUSG00000058435	Btnl4	Btn3a3|EG632126|NG11	butyrophilin-like 4	protein-coding
Merged-chr1-145966258-1	chr1	145966108	145966408	+	1	NA	Intergenic	L1Md_A|LINE|L1	-529371	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr10-80286917-1	chr10	80286833	80287002	+	1	NA	intron (NM_133188, intron 11 of 11)	intron (NM_133188, intron 11 of 11)	-5514	NM_009091	20054	Mm.643	NM_009091	ENSMUSG00000063457	Rps15	rig	ribosomal protein S15	protein-coding
Merged-chr1-108323766-1	chr1	108323687	108323845	+	1	NA	Intergenic	L1Md_T|LINE|L1	406507	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr1-52405645-1	chr1	52405507	52405784	+	1	NA	Intergenic	L1Md_T|LINE|L1	94803	NM_008667	17936	Mm.25903	NM_008667	ENSMUSG00000002881	Nab1	-	Ngfi-A binding protein 1	protein-coding
Merged-chr13-67970258-1	chr13	67970128	67970388	+	1	NA	Intergenic	Intergenic	106932	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr19-21343935-1	chr19	21343837	21344034	+	1	NA	Intergenic	L1Md_F3|LINE|L1	71657	NM_009551	22682	Mm.292405	NM_009551	ENSMUSG00000024750	Zfand5	2310057A04Rik|5830475F03Rik|AA415485|Za20d2|Zfp216	zinc finger, AN1-type domain 5	protein-coding
Merged-chr13-66703457-1	chr13	66703257	66703658	+	1	NA	Intergenic	Intergenic	201893	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-109038667-1	chr1	109038557	109038777	+	1	NA	Intergenic	L1Md_T|LINE|L1	-944233	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr6-7920729-1	chr6	7920633	7920825	+	1	NA	Intergenic	L1Md_A|LINE|L1	75505	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
Merged-chr15-97831060-1	chr15	97830981	97831140	+	1	NA	intron (NM_001204276, intron 1 of 25)	CpG	707	NM_001204276	56233	Mm.384027	NM_019572	ENSMUSG00000022475	Hdac7	5830434K02Rik|HD7|HD7a|Hdac7a|mFLJ00062	histone deacetylase 7	protein-coding
Merged-chr15-98804188-1	chr15	98804082	98804294	+	1	NA	3' UTR (NM_001013741, exon 2 of 2)	3' UTR (NM_001013741, exon 2 of 2)	3737	NM_001013741	13199	Mm.390810	NM_001013741	ENSMUSG00000059213	Ddn	Gm748	dendrin	protein-coding
Merged-chr12-9632652-1	chr12	9632562	9632743	+	1	NA	Intergenic	L1Md_T|LINE|L1	58210	NM_011859	23967	Mm.45055	NM_011859	ENSMUSG00000048387	Osr1	Odd1|Osr	odd-skipped related transcription factor 1	protein-coding
Merged-chr1-165406851-1	chr1	165406751	165406952	+	1	NA	intron (NM_028759, intron 6 of 18)	L1Md_Gf|LINE|L1	53612	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
Merged-chr1-47246114-1	chr1	47245998	47246230	+	1	NA	Intergenic	L1Md_A|LINE|L1	221011	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr14-51597780-1	chr14	51597618	51597942	+	1	NA	intron (NM_001013816, intron 1 of 4)	L1_Mus3|LINE|L1	44990	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chrX-102247702-1	chrX	102247622	102247783	+	1	NA	exon (NM_001276473, exon 3 of 3)	exon (NM_001276473, exon 3 of 3)	3074	NM_001276473	12705	Mm.2390	NM_007709	ENSMUSG00000051159	Cited1	AI316840|AU019144|Msg1	Cbp/p300-interacting transactivator with Glu/Asp-rich carboxy-terminal domain 1	protein-coding
Merged-chr15-96949985-1	chr15	96949895	96950075	+	1	NA	Intergenic	Intergenic	70374	NM_001358059	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
Merged-chr15-74847414-1	chr15	74847334	74847495	+	1	NA	Intergenic	Lx3C|LINE|L1	-5771	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
Merged-chr12-115641633-1	chr12	115641450	115641816	+	1	NA	Intergenic	Lx7|LINE|L1	54161	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-75658457-1	chr11	75658363	75658551	+	1	NA	exon (NM_008659, exon 4 of 32)	exon (NM_008659, exon 4 of 32)	2442	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
Merged-chr11-75657681-1	chr11	75657492	75657870	+	1	NA	intron (NM_001080774, intron 2 of 31)	intron (NM_001080774, intron 2 of 31)	1666	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
Merged-chr10-121944078-1	chr10	121943986	121944171	+	1	NA	intron (NM_001081037, intron 1 of 21)	L1Md_T|LINE|L1	103237	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
Merged-chr12-14453324-1	chr12	14453163	14453485	+	1	NA	Intergenic	L1Md_T|LINE|L1	191790	NR_045003	791361	Mm.217963	NR_045003	ENSMUSG00000113336	Gm16497	-	predicted gene 16497	ncRNA
Merged-chr1-40198299-1	chr1	40198056	40198542	+	1	NA	Intergenic	L1Md_T|LINE|L1	-26781	NM_008362	16177	Mm.896	NM_008362	ENSMUSG00000026072	Il1r1	CD121a|CD121b|IL-1R1|IL-iR|Il1r-1	interleukin 1 receptor, type I	protein-coding
Merged-chr13-66588162-1	chr13	66588070	66588254	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-147044	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr14-51592360-1	chr14	51592262	51592458	+	1	NA	intron (NM_001013816, intron 1 of 4)	intron (NM_001013816, intron 1 of 4)	39570	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr8-119336935-1	chr8	119336782	119337089	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-7603	NM_024219	68196	Mm.358714	NM_024219	ENSMUSG00000031839	Hsbp1	0610007A03Rik|AA408769|Hsp25	heat shock factor binding protein 1	protein-coding
Merged-chr4-62523528-1	chr4	62523338	62523719	+	1	NA	TTS (NM_021498)	TTS (NM_021498)	1486	NM_021498	59001	Mm.27444	NM_021498	ENSMUSG00000028394	Pole3	1810034K18Rik|YBL1	polymerase (DNA directed), epsilon 3 (p17 subunit)	protein-coding
Merged-chr11-25558366-1	chr11	25558257	25558475	+	1	NA	Intergenic	L1Md_A|LINE|L1	232259	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	ncRNA
Merged-chr5-26033124-1	chr5	26032953	26033295	+	1	NA	Intergenic	BGLII_B|LTR|ERVK	6381	NM_029376	75657	Mm.374273	NM_029376	ENSMUSG00000073119	Speer4a	1700027N01Rik|SPEER-4A	spermatogenesis associated glutamate (E)-rich protein 4A	protein-coding
Merged-chr1-18540720-1	chr1	18540324	18541117	+	1	NA	Intergenic	L1Md_T|LINE|L1	-275582	NM_183124	77673	Mm.99530	NM_183124	ENSMUSG00000067773	Defb41	9230102D03Rik|BD-17|Bd-41|Defb16|Defb17|Gm15386	defensin beta 41	protein-coding
Merged-chr11-41385906-1	chr11	41385772	41386040	+	1	NA	Intergenic	L1Md_A|LINE|L1	614808	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
Merged-chr15-25197074-1	chr15	25196976	25197173	+	1	NA	Intergenic	L1Md_F2|LINE|L1	216690	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
Merged-chr11-45097294-1	chr11	45097013	45097575	+	1	NA	Intergenic	L1Md_T|LINE|L1	19634	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA
Merged-chr15-58704253-1	chr15	58704175	58704331	+	1	NA	Intergenic	RMER13A|LTR|ERVK	119174	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
Merged-chr10-129590439-1	chr10	129590342	129590536	+	1	NA	Intergenic	L1Md_T|LINE|L1	18040	NM_146931	258933	Mm.377755	NM_146931	ENSMUSG00000052012	Olfr796	MOR269-1	olfactory receptor 796	protein-coding
Merged-chr12-115614663-1	chr12	115614522	115614804	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	81131	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr15-102161646-1	chr15	102161553	102161739	+	1	NA	intron (NM_146064, intron 12 of 14)	B1_Mus2|SINE|Alu	11071	NM_146064	223920	Mm.358862	NM_146064	ENSMUSG00000023045	Soat2	ACAT2|D15Wsu97e	sterol O-acyltransferase 2	protein-coding
Merged-chr15-82110004-1	chr15	82109921	82110087	+	1	NA	intron (NM_028897, intron 22 of 30)	intron (NM_028897, intron 22 of 30)	-17918	NM_001326588	76457	Mm.440373	NM_172428	ENSMUSG00000068114	Ccdc134	2310042L06Rik|AW208859	coiled-coil domain containing 134	protein-coding
Merged-chr15-77624849-1	chr15	77624733	77624966	+	1	NA	Intergenic	Intergenic	18437	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr1-5823289-1	chr1	5823187	5823392	+	1	NA	Intergenic	L1Md_A|LINE|L1	94109	NM_010342	226304	Mm.291110	NM_010342	ENSMUSG00000033774	Npbwr1	Gpr7|Nbpwr1	neuropeptides B/W receptor 1	protein-coding
Merged-chr4-51654335-1	chr4	51654237	51654434	+	1	NA	Intergenic	L1Md_T|LINE|L1	396775	NR_040668	329844	Mm.128934	NR_040668	ENSMUSG00000085515	C630028M04Rik	-	RIKEN cDNA C630028M04 gene	ncRNA
Merged-chr19-3948881-1	chr19	3948775	3948988	+	1	NA	exon (NM_019449, exon 11 of 11)	exon (NM_019449, exon 11 of 11)	-9927	NM_028545	73458	Mm.482922	NM_028545	ENSMUSG00000037263	Aldh3b3	1700055N04Rik	aldehyde dehydrogenase 3 family, member B3	protein-coding
Merged-chr1-42337538-1	chr1	42337395	42337681	+	1	NA	Intergenic	L1Md_T|LINE|L1	357287	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
Merged-chr13-64585958-1	chr13	64585872	64586045	+	1	NA	Intergenic	L1Md_A|LINE|L1	-88166	NM_001195435	68880	Mm.390594	NM_001195435	ENSMUSG00000096537	Fam240b	1190003K10Rik	family with sequence similarity 240 member B	protein-coding
Merged-chr12-116543244-1	chr12	116543163	116543326	+	1	NA	intron (NM_011215, intron 1 of 22)	L1Md_A|LINE|L1	57524	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
Merged-chr1-130324360-1	chr1	130324262	130324458	+	1	NA	Intergenic	L1Md_T|LINE|L1	-98464	NR_151525	102640368		NR_151525	ENSMUSG00000087691	Gm15674	-	predicted gene 15674	ncRNA
Merged-chr1-25123621-1	chr1	25123505	25123738	+	1	NA	intron (NM_175642, intron 22 of 30)	L1Md_Gf|LINE|L1	154333	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
Merged-chr9-19160199-1	chr9	19160080	19160319	+	1	NA	Intergenic	L1Md_T|LINE|L1	23271	NM_146565	258558	Mm.377567	NM_146565	ENSMUSG00000110621	Olfr837	MOR152-2	olfactory receptor 837	protein-coding
Merged-chr12-30192023-1	chr12	30191941	30192105	+	1	NA	intron (NM_001324521, intron 15 of 15)	L1Md_T|LINE|L1	-59399	NM_009417	22018	Mm.4991	NM_009417	ENSMUSG00000020673	Tpo	-	thyroid peroxidase	protein-coding
Merged-chr8-11934889-1	chr8	11934777	11935001	+	1	NA	Intergenic	L1Md_F2|LINE|L1	94368	NM_029326	75528	Mm.440342	NM_029326	ENSMUSG00000031512	Tex29	1700018L24Rik	testis expressed 29	protein-coding
Merged-chr10-78945296-1	chr10	78945135	78945458	+	1	NA	Intergenic	L1Md_T|LINE|L1	-9911	NM_207201	18372	Mm.391567	NM_207201	ENSMUSG00000094080	Olfr8	GA_x5J8B7TNKDU-1250-1574|MOR139-5P	olfactory receptor 8	protein-coding
Merged-chr12-68436000-1	chr12	68435885	68436116	+	1	NA	Intergenic	L1Md_T|LINE|L1	723186	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr12-62230410-1	chr12	62230306	62230514	+	1	NA	Intergenic	L1Md_A|LINE|L1	-457377	NR_131949	73309	Mm.276558	NR_131949		Spanxn4	1700047L15Rik	SPANX family, member N4	ncRNA
Merged-chr10-109407576-1	chr10	109407483	109407670	+	1	NA	Intergenic	L1Md_T|LINE|L1	-396601	NM_009306	20979	Mm.289702	NM_009306	ENSMUSG00000035864	Syt1	AW124717|G630098F17Rik|SytI	synaptotagmin I	protein-coding
Merged-chr13-62124020-1	chr13	62123903	62124138	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	-5870	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr15-85580437-1	chr15	85580357	85580517	+	1	NA	promoter-TSS (NR_040433)	promoter-TSS (NR_040433)	292	NM_001163633	22422	Mm.306946	NM_009528	ENSMUSG00000022382	Wnt7b	Wnt-7b	wingless-type MMTV integration site family, member 7B	protein-coding
Merged-chr1-54030698-1	chr1	54030537	54030859	+	1	NA	intron (NM_001001883, intron 2 of 28)	L1Md_T|LINE|L1	164336	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
Merged-chr5-25937735-1	chr5	25937554	25937917	+	1	NA	Intergenic	Intergenic	16609	NM_001281516	100862359		NM_001281516	ENSMUSG00000095550	Gm21671	-	predicted gene, 21671	protein-coding
Merged-chr13-17932322-1	chr13	17932227	17932418	+	1	NA	intron (NM_019491, intron 1 of 4)	MT2_Mm|LTR|ERVL	11895	NM_019491	56044	Mm.27348	NM_019491	ENSMUSG00000008859	Rala	3010001O15Rik|AW322615|Ral|Rasl1	v-ral simian leukemia viral oncogene A (ras related)	protein-coding
Merged-chr15-60594411-1	chr15	60594310	60594513	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-228554	NR_030696	320469	Mm.230853	NM_177166		9930014A18Rik	-	RIKEN cDNA 9930014A18 gene	ncRNA
Merged-chr15-24411796-1	chr15	24411693	24411900	+	1	NA	Intergenic	L1Md_F|LINE|L1	1001968	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
Merged-chr15-79984233-1	chr15	79984087	79984379	+	1	NA	Intergenic	Intergenic	14793	NR_106072	102465699		NR_106072	ENSMUSG00000099222	Mir7213	Gm27377|mmu-mir-7213	microRNA 7213	ncRNA
Merged-chr1-185157916-1	chr1	185157817	185158016	+	1	NA	Intergenic	L1Md_T|LINE|L1	-46252	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
Merged-chr1-15262693-1	chr1	15262592	15262794	+	1	NA	Intergenic	L1Md_T|LINE|L1	-49759	NM_001098528	98741	Mm.156081	NM_001033195	ENSMUSG00000092083	Kcnb2	9630047L19Rik|BB130875|Kv2.2	potassium voltage gated channel, Shab-related subfamily, member 2	protein-coding
Merged-chr1-32779671-1	chr1	32779578	32779765	+	1	NA	Intergenic	L1Md_T|LINE|L1	-232378	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr1-84573907-1	chr1	84573822	84573992	+	1	NA	intron (NM_152915, intron 4 of 12)	L1Md_T|LINE|L1	-121932	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
Merged-chr19-5047727-1	chr19	5047617	5047838	+	1	NA	intron (NM_134155, intron 7 of 9)	intron (NM_134155, intron 7 of 9)	-3081	NM_145495	225870	Mm.271922	NM_145495	ENSMUSG00000024883	Rin1	-	Ras and Rab interactor 1	protein-coding
Merged-chr10-96509040-1	chr10	96508832	96509248	+	1	NA	Intergenic	L1Md_T|LINE|L1	-107961	NM_007569	12226	Mm.23811	NM_007569	ENSMUSG00000036478	Btg1	AI426953|AW546738	B cell translocation gene 1, anti-proliferative	protein-coding
Merged-chr13-66774353-1	chr13	66774272	66774434	+	1	NA	Intergenic	Intergenic	130997	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr12-115506100-1	chr12	115506013	115506187	+	1	NA	Intergenic	Lx2B2|LINE|L1	189694	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-32669433-1	chr1	32669290	32669577	+	1	NA	Intergenic	L1Md_T|LINE|L1	-122140	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr17-38553346-1	chr17	38553190	38553502	+	1	NA	promoter-TSS (NM_001177585)	promoter-TSS (NM_001177585)	-846	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr11-13311564-1	chr11	13311367	13311762	+	1	NA	Intergenic	L1Md_T|LINE|L1	-846604	NM_001282993	12808	Mm.22847	NM_172496	ENSMUSG00000020173	Cobl	-	cordon-bleu WH2 repeat	protein-coding
Merged-chr15-58872993-1	chr15	58872900	58873086	+	1	NA	exon (NM_026642, exon 1 of 1)	exon (NM_026642, exon 1 of 1)	344	NM_026642	68260	Mm.278805	NM_026642	ENSMUSG00000037085	Trmt12	4632406N01Rik|AI449275|Tyw2	tRNA methyltranferase 12	protein-coding
Merged-chr10-80549313-1	chr10	80549201	80549425	+	1	NA	intron (NM_025852, intron 2 of 14)	intron (NM_025852, intron 2 of 14)	-10189	NM_026094	67331	Mm.52511	NM_026094	ENSMUSG00000003341	Atp8b3	1700042F02Rik|1700056N23Rik|ATPIK|SAPLT	ATPase, class I, type 8B, member 3	protein-coding
Merged-chr19-15830806-1	chr19	15830727	15830885	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	93816	NM_001205339	107272	Mm.289936	NM_177420	ENSMUSG00000024640	Psat1	D8Ertd814e|EPIP|PSA|Psat	phosphoserine aminotransferase 1	protein-coding
Merged-chr19-10057251-1	chr19	10057143	10057360	+	1	NA	intron (NM_021890, intron 11 of 11)	intron (NM_021890, intron 11 of 11)	15703	NM_021890	60527	Mm.253875	NM_021890	ENSMUSG00000024664	Fads3	AI464531	fatty acid desaturase 3	protein-coding
Merged-chr19-13245393-1	chr19	13245252	13245535	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	11141	NM_001011840	258120	Mm.329753	NM_001011840	ENSMUSG00000096365	Olfr1463	MOR202-29P	olfactory receptor 1463	protein-coding
Merged-chr1-144811913-1	chr1	144811829	144811997	+	1	NA	Intergenic	L1Md_A|LINE|L1	-36486	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr15-82755510-1	chr15	82755432	82755588	+	1	NA	Intergenic	Lx3B|LINE|L1	8612	NM_023623	71754	Mm.443024	NM_023623	ENSMUSG00000068083	Cyp2d40	1300013D18Rik|CYPIID3|P450-DB3	cytochrome P450, family 2, subfamily d, polypeptide 40	protein-coding
Merged-chr15-76669108-1	chr15	76668989	76669228	+	1	NA	TTS (NM_001358912)	TTS (NM_001358912)	840	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
Merged-chr14-35370657-1	chr14	35370572	35370743	+	1	NA	intron (NM_008166, intron 8 of 15)	L1Md_A|LINE|L1	441321	NM_001033766	239036	Mm.239970	NM_001033766	ENSMUSG00000041068	4930596D02Rik	-	RIKEN cDNA 4930596D02 gene	protein-coding
Merged-chr13-106804404-1	chr13	106804287	106804522	+	1	NA	intron (NM_001360897, intron 30 of 30)	intron (NM_001360897, intron 30 of 30)	132554	NM_001360897	76582	Mm.132208	NM_029665	ENSMUSG00000042590	Ipo11	1700081H05Rik|2510001A17Rik|AI314624|AW555235|E330021B14Rik|Ranbp11	importin 11	protein-coding
Merged-chr19-6057909-1	chr19	6057807	6058011	+	1	NA	promoter-TSS (NM_001160239)	promoter-TSS (NM_001160239)	21	NM_001160239	14109	Mm.329631	NM_007990	ENSMUSG00000038274	Fau	MNSFbeta	Finkel-Biskis-Reilly murine sarcoma virus (FBR-MuSV) ubiquitously expressed (fox derived)	protein-coding
Merged-chr17-38521417-1	chr17	38521330	38521504	+	1	NA	Intergenic	Intergenic	-32775	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr15-80111731-1	chr15	80111588	80111874	+	1	NA	exon (NM_009303, exon 3 of 4)	exon (NM_009303, exon 3 of 4)	20397	NM_009303	20972	Mm.230301	NM_009303	ENSMUSG00000022415	Syngr1	R75468|Syngr1b|p29	synaptogyrin 1	protein-coding
Merged-chr1-61676902-1	chr1	61676824	61676981	+	1	NA	intron (NM_001081050, intron 1 of 22)	L1Md_A|LINE|L1	38078	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
Merged-chr2-156389627-1	chr2	156389499	156389756	+	1	NA	non-coding (NR_024329, exon 1 of 1)	non-coding (NR_024329, exon 1 of 1)	3352	NR_024329	347740	Mm.324242	NR_024329	ENSMUSG00000102869	2900097C17Rik	1810005K14Rik|4930563C06Rik	RIKEN cDNA 2900097C17 gene	ncRNA
Merged-chr1-19376923-1	chr1	19376804	19377043	+	1	NA	Intergenic	L1Md_T|LINE|L1	164869	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr10-17463036-1	chr10	17462829	17463244	+	1	NA	Intergenic	L1Md_A|LINE|L1	-260192	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
Merged-chr8-74982626-1	chr8	74982514	74982738	+	1	NA	Intergenic	Intergenic	-11024	NM_178017	70823	Mm.261739	NM_178017	ENSMUSG00000034518	Hmgxb4	4733401K04Rik|AI316803|Hmgb2l1	HMG box domain containing 4	protein-coding
Merged-chr12-90963304-1	chr12	90963124	90963485	+	1	NA	Intergenic	L1Md_T|LINE|L1	-82544	NR_045858	71349	Mm.442093	NR_045858	ENSMUSG00000085004	5430427M07Rik	-	RIKEN cDNA 5430427M07 gene	ncRNA
Merged-chr10-55500291-1	chr10	55500044	55500538	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	-606626	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr13-100271557-1	chr13	100271461	100271653	+	1	NA	Intergenic	L1_Rod|LINE|L1	-24221	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
Merged-chr17-38505730-1	chr17	38505565	38505895	+	1	NA	Intergenic	L1_Mur2|LINE|L1	-48462	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr1-104276010-1	chr1	104275910	104276110	+	1	NA	Intergenic	L1Md_T|LINE|L1	-492510	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr10-23472848-1	chr10	23472746	23472951	+	1	NA	Intergenic	L1Md_T|LINE|L1	-122905	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
Merged-chr13-36667355-1	chr13	36667246	36667465	+	1	NA	Intergenic	L1Md_T|LINE|L1	67122	NM_153529	68404	Mm.232930	NM_153529	ENSMUSG00000039114	Nrn1	0710008J23Rik|Cpg15|Nrn	neuritin 1	protein-coding
Merged-chr1-25594576-1	chr1	25594389	25594763	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	235131	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr7-59364752-1	chr7	59364575	59364930	+	1	NA	intron (NR_146211, intron 147 of 171)	intron (NR_146211, intron 147 of 171)	-17328	NR_146600	102642160		NR_146600		Gm22496	-	predicted gene, 22496	snoRNA
Merged-chr10-10956605-1	chr10	10956490	10956721	+	1	NA	intron (NM_001114333, intron 2 of 9)	L1Md_T|LINE|L1	125726	NM_016976	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
Merged-chr15-66660152-1	chr15	66660023	66660282	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-10618	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
Merged-chr1-96574169-1	chr1	96574065	96574274	+	1	NA	Intergenic	L1Md_A|LINE|L1	88404	NR_040478	75159	Mm.243854	NR_040478	ENSMUSG00000100589	4930533P14Rik	-	RIKEN cDNA 4930533P14 gene	ncRNA
Merged-chr14-11344016-1	chr14	11343926	11344107	+	1	NA	Intergenic	L1Md_F2|LINE|L1	61539	NR_105811	102466641		NR_105811	ENSMUSG00000099218	Mir5124b	Gm27681|mmu-mir-5124b	microRNA 5124b	ncRNA
Merged-chr17-23330356-1	chr17	23330224	23330489	+	1	NA	Intergenic	Lx7|LINE|L1	-13621	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr19-29687147-1	chr19	29687048	29687246	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-10794	NM_029993	77836	Mm.138437	NM_029993	ENSMUSG00000024806	Mlana	A930034P04Rik|Mart1	melan-A	protein-coding
Merged-chr13-66618764-1	chr13	66618572	66618956	+	1	NA	Intergenic	RLTR18-int|LTR|ERVK	-177646	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr19-5570231-1	chr19	5570145	5570317	+	1	NA	exon (NM_001033448, exon 2 of 2)	exon (NM_001033448, exon 2 of 2)	2207	NM_001033448	381201	Mm.441906	NM_001033448	ENSMUSG00000049562	Ap5b1	Gm962|beta-5	adaptor-related protein complex 5, beta 1 subunit	protein-coding
Merged-chr11-34878712-1	chr11	34878616	34878809	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-45071	NM_027411	70385	Mm.194368	NM_027411	ENSMUSG00000069910	Spdl1	1700018I02Rik|2600001J17Rik|2810049B11Rik|AA409762|Ccdc99	spindle apparatus coiled-coil protein 1	protein-coding
Merged-chr1-24076852-1	chr1	24076754	24076951	+	1	NA	intron (NM_026604, intron 3 of 20)	L1Md_T|LINE|L1	23489	NM_026604	68187	Mm.87130	NM_026604	ENSMUSG00000026153	Fam135a	4921533L14Rik|AI256732|AI835491	family with sequence similarity 135, member A	protein-coding
Merged-chr19-5696256-1	chr19	5696132	5696380	+	1	NA	intron (NM_022012, intron 7 of 11)	CpG	7125	NM_022012	26403	Mm.185026	NM_022012	ENSMUSG00000004054	Map3k11	2610017K16Rik|Mlk3|PTK1|SPRK	mitogen-activated protein kinase kinase kinase 11	protein-coding
Merged-chr1-171547565-1	chr1	171547309	171547822	+	1	NA	Intergenic	MT2B1|LTR|ERVL	-11628	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
Merged-chr13-73792443-1	chr13	73792365	73792522	+	1	NA	intron (NM_001360694, intron 6 of 24)	intron (NM_001360694, intron 6 of 24)	28746	NM_011390	20499	Mm.275800	NM_011390	ENSMUSG00000017756	Slc12a7	AA408796|D13Ertd261e|Kcc4	solute carrier family 12, member 7	protein-coding
Merged-chr7-122915958-1	chr7	122915865	122916052	+	1	NA	Intergenic	MERVL-int|LTR|ERVL	54501	NR_045614	73951	Mm.389936	NR_045614		4930413G21Rik	-	RIKEN cDNA 4930413G21 gene	ncRNA
Merged-chr19-3434486-1	chr19	3434391	3434581	+	1	NA	Intergenic	Intergenic	-19942	NM_001329667	14419	Mm.4655	NM_010253	ENSMUSG00000024907	Gal	Galn	galanin	protein-coding
Merged-chr19-28426094-1	chr19	28425972	28426217	+	1	NA	intron (NM_175459, intron 4 of 10)	(CA)n|Simple_repeat|Simple_repeat	-252130	NR_045330	320176	Mm.406716	NR_045330	ENSMUSG00000097735	D930032P07Rik	-	RIKEN cDNA D930032P07 gene	ncRNA
Merged-chr19-5943515-1	chr19	5943410	5943620	+	1	NA	intron (NM_001164057, intron 14 of 17)	intron (NM_001164057, intron 14 of 17)	-18699	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
Merged-chr11-17515042-1	chr11	17514811	17515273	+	1	NA	Intergenic	L1Md_T|LINE|L1	257354	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
Merged-chr10-37732210-1	chr10	37732131	37732289	+	1	NA	Intergenic	L1Md_A|LINE|L1	-443564	NR_131035	75877	Mm.402094	NR_131035	ENSMUSG00000111234	4930591E09Rik	-	RIKEN cDNA 4930591E09 gene	ncRNA
Merged-chrX-3220037-1	chrX	3219959	3220115	+	1	NA	Intergenic	L1Md_F2|LINE|L1	143117	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr1-72546854-1	chr1	72546739	72546970	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10290	NM_001045533	381270	Mm.337023	NM_001045533	ENSMUSG00000039372	March4	BC056494|mKIAA1399	membrane-associated ring finger (C3HC4) 4	protein-coding
Merged-chr19-6046962-1	chr19	6046832	6047092	+	1	NA	promoter-TSS (NM_001164709)	promoter-TSS (NM_001164709)	-183	NM_001164709	74126	Mm.149870	NM_028769	ENSMUSG00000024807	Syvn1	1200010C09Rik|AW211966|C85322|D530017H19Rik|Hrd1	synovial apoptosis inhibitor 1, synoviolin	protein-coding
Merged-chr17-27237420-1	chr17	27237247	27237593	+	1	NA	intron (NR_131118, intron 2 of 2)	intron (NR_131118, intron 2 of 2)	10646	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
Merged-chr10-116028835-1	chr10	116028755	116028915	+	1	NA	intron (NM_011217, intron 1 of 13)	L1Md_T|LINE|L1	10472	NM_011217	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
Merged-chr1-160427342-1	chr1	160427212	160427472	+	1	NA	intron (NM_013862, intron 17 of 20)	L1Md_A|LINE|L1	-75771	NM_001038621	29809	Mm.25833	NM_013862	ENSMUSG00000026721	Rabgap1l	5830411O09Rik|8430421H08Rik|9630005B12Rik|AW049894|HHL|Hh1|mKIAA0471	RAB GTPase activating protein 1-like	protein-coding
Merged-chr15-76986760-1	chr15	76986633	76986887	+	1	NA	Intergenic	Intergenic	35967	NM_001164048	17189	Mm.404074	NM_013593	ENSMUSG00000018893	Mb	AI325109	myoglobin	protein-coding
Merged-chr15-95812502-1	chr15	95812361	95812643	+	1	NA	intron (NM_175344, intron 1 of 19)	intron (NM_175344, intron 1 of 19)	17570	NR_155277	102634389	Mm.440563	NR_155276	ENSMUSG00000078648	LOC102634389	-	uncharacterized LOC102634389	ncRNA
Merged-chr17-38556261-1	chr17	38556151	38556371	+	1	NA	intron (NM_001177585, intron 2 of 2)	MTA_Mm|LTR|ERVL-MaLR	2069	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr15-74975646-1	chr15	74975565	74975728	+	1	NA	Intergenic	A-rich|Low_complexity|Low_complexity	7784	NM_001358005	57248	Mm.358339	NM_020498	ENSMUSG00000022586	Ly6i	AI789751|Ly-6I|Ly-6M	lymphocyte antigen 6 complex, locus I	protein-coding
Merged-chr19-5851794-1	chr19	5851689	5851899	+	1	NA	3' UTR (NM_026169, exon 11 of 11)	3' UTR (NM_026169, exon 11 of 11)	-6314	NR_003513	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
Merged-chr4-69712002-1	chr4	69711905	69712100	+	1	NA	Intergenic	L1Md_T|LINE|L1	698433	NM_001313762	214444	Mm.370777	NM_145990	ENSMUSG00000039298	Cdk5rap2	2900018K03Rik|an|mKIAA1633	CDK5 regulatory subunit associated protein 2	protein-coding
Merged-chrX-115580099-1	chrX	115579965	115580234	+	1	NA	Intergenic	L1Md_A|LINE|L1	653110	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
Merged-chr11-26733949-1	chr11	26733848	26734051	+	1	NA	Intergenic	L1Md_T|LINE|L1	-51159	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr4-52683414-1	chr4	52683294	52683534	+	1	NA	Intergenic	RLTR6_Mm|LTR|ERV1	76208	NM_001356293	68274	Mm.85045	NM_026652	ENSMUSG00000028314	Toporsl	4930547C10Rik	topoisomerase I binding, arginine/serine-rich like	protein-coding
Merged-chr15-52772606-1	chr15	52772449	52772763	+	1	NA	Intergenic	L1Md_F2|LINE|L1	60161	NM_027212	69790	Mm.195562	NM_027212	ENSMUSG00000038622	Med30	1810038N03Rik|2510044J04Rik|TRAP25|Thrap6	mediator complex subunit 30	protein-coding
Merged-chr7-7512788-1	chr7	7512701	7512876	+	1	NA	Intergenic	Lx2|LINE|L1	-32815	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr19-5457309-1	chr19	5456981	5457638	+	1	NA	exon (NM_198616, exon 1 of 1)	exon (NM_198616, exon 1 of 1)	254	NM_198616	240514	Mm.329657	NM_198616	ENSMUSG00000095098	Ccdc85b	AI842788|BB115872	coiled-coil domain containing 85B	protein-coding
Merged-chr1-48285835-1	chr1	48285757	48285913	+	1	NA	Intergenic	L1Md_T|LINE|L1	-818710	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr13-67944837-1	chr13	67944755	67944919	+	1	NA	Intergenic	Intergenic	81511	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr10-79988779-1	chr10	79988664	79988894	+	1	NA	intron (NM_007725, intron 1 of 6)	CpG	179	NM_007725	12798	Mm.157770	NM_007725	ENSMUSG00000004665	Cnn2	AA408047|AI324678|Calpo2	calponin 2	protein-coding
Merged-chr1-147283097-1	chr1	147283012	147283182	+	1	NA	Intergenic	L1Md_A|LINE|L1	785410	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr19-6157092-1	chr19	6156994	6157191	+	1	NA	Intergenic	Intergenic	-7347	NM_001356604	74481	Mm.159219	NM_028967	ENSMUSG00000039699	Batf2	B-ATF-2	basic leucine zipper transcription factor, ATF-like 2	protein-coding
Merged-chr13-5141529-1	chr13	5141392	5141667	+	1	NA	Intergenic	L1Md_A|LINE|L1	-532365	NM_018859	56043	Mm.251908	NM_018859	ENSMUSG00000045410	Akr1e1	1810061I10Rik|Akr1e2	aldo-keto reductase family 1, member E1	protein-coding
Merged-chr10-114332616-1	chr10	114332532	114332700	+	1	NA	Intergenic	L1Md_T|LINE|L1	468754	NM_146241	237553	Mm.445550	NM_146241	ENSMUSG00000050663	Trhde	9330155P21Rik	TRH-degrading enzyme	protein-coding
Merged-chr5-25933796-1	chr5	25933633	25933959	+	1	NA	Intergenic	Intergenic	20548	NM_001281516	100862359		NM_001281516	ENSMUSG00000095550	Gm21671	-	predicted gene, 21671	protein-coding
Merged-chr13-68020087-1	chr13	68019876	68020299	+	1	NA	Intergenic	Lx2|LINE|L1	156761	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr13-68026738-1	chr13	68026422	68027055	+	1	NA	Intergenic	RLTR45|LTR|ERVK	163412	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chrX-44442609-1	chrX	44442516	44442702	+	1	NA	Intergenic	L1Md_A|LINE|L1	-74272	NM_175539	245403	Mm.55270	NM_175539	ENSMUSG00000050926	Dcaf12l2	A130007F10Rik|Wdr40c	DDB1 and CUL4 associated factor 12-like 2	protein-coding
Merged-chr10-128956747-1	chr10	128956655	128956839	+	1	NA	intron (NM_008398, intron 24 of 24)	RLTR17B_Mm|LTR|ERVK	4241	NM_027853	71664	Mm.337232	NM_027853	ENSMUSG00000025347	Mettl7b	0610006F02Rik|AI266817	methyltransferase like 7B	protein-coding
Merged-chr7-59364227-1	chr7	59364133	59364322	+	1	NA	intron (NR_146211, intron 147 of 171)	intron (NR_146211, intron 147 of 171)	-16803	NR_146600	102642160		NR_146600		Gm22496	-	predicted gene, 22496	snoRNA
Merged-chr15-89504833-1	chr15	89504705	89504961	+	1	NA	intron (NM_021423, intron 8 of 21)	intron (NM_021423, intron 8 of 21)	4976	NM_021423	58234	Mm.146855	NM_021423	ENSMUSG00000022623	Shank3	AI841104|SHANK3c-3|SHANK3c-4|Shank3b	SH3 and multiple ankyrin repeat domains 3	protein-coding
Merged-chr1-145470431-1	chr1	145470346	145470516	+	1	NA	Intergenic	L1Md_T|LINE|L1	-695004	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr13-17152987-1	chr13	17152880	17153095	+	1	NA	intron (NM_138654, intron 12 of 13)	L1Md_A|LINE|L1	541778	NM_138654	192136	Mm.364180	NM_138654	ENSMUSG00000055137	Sugct	5033411D12Rik|D17907	succinyl-CoA glutarate-CoA transferase	protein-coding
Merged-chr10-22326287-1	chr10	22326126	22326448	+	1	NA	intron (NM_009018, intron 6 of 6)	L1Md_F|LINE|L1	19567	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
Merged-chrX-67032830-1	chrX	67032687	67032973	+	1	NA	Intergenic	L1_Mus2|LINE|L1	-193705	NR_030149	723888		NR_030149	ENSMUSG00000070071	Mir465	Mirn465|mir-465a|mmu-mir-465	microRNA 465	ncRNA
Merged-chr1-82551556-1	chr1	82551381	82551732	+	1	NA	intron (NM_007735, intron 4 of 47)	L1Md_A|LINE|L1	35293	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
Merged-chr19-57369988-1	chr19	57369907	57370070	+	1	NA	intron (NM_145505, intron 2 of 16)	intron (NM_145505, intron 2 of 16)	8979	NM_145505	226252	Mm.358870	NM_145505	ENSMUSG00000033478	Fam160b1	AI450540|mKIAA1600	family with sequence similarity 160, member B1	protein-coding
Merged-chr15-55072026-1	chr15	55071895	55072157	+	1	NA	5' UTR (NM_001081288, exon 1 of 26)	5' UTR (NM_001081288, exon 1 of 26)	126	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
Merged-chrX-124120206-1	chrX	124119936	124120476	+	1	NA	Intergenic	L1_Mus3|LINE|L1	15704	NM_001100616	100038941	Mm.388852	NM_001100616	ENSMUSG00000072049	Vmn2r121	EG625699	vomeronasal 2, receptor 121	protein-coding
Merged-chr11-37754626-1	chr11	37754338	37754915	+	1	NA	Intergenic	L1Md_T|LINE|L1	95637	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr12-46997392-1	chr12	46997228	46997557	+	1	NA	Intergenic	(CAGAG)n|Simple_repeat|Simple_repeat	-178617	NM_021361	664883	Mm.247195	NM_021361	ENSMUSG00000021047	Nova1	9430099M15Rik|G630039L02|Nova-1	neuro-oncological ventral antigen 1	protein-coding
Merged-chr15-32290090-1	chr15	32290002	32290179	+	1	NA	intron (NM_009154, intron 1 of 22)	intron (NM_009154, intron 1 of 22)	45277	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
Merged-chr19-4409946-1	chr19	4409862	4410030	+	1	NA	Intergenic	Intergenic	-12869	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
Merged-chr8-16794282-1	chr8	16794191	16794374	+	1	NA	intron (NM_053171, intron 3 of 69)	IAPEz-int|LTR|ERVK	-625444	NR_037214	100526464		NR_037214	ENSMUSG00000093142	Mir3106	mir-3106|mmu-mir-3106	microRNA 3106	ncRNA
Merged-chr17-74906713-1	chr17	74906501	74906926	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-98816	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
Merged-chr14-79835324-1	chr14	79835226	79835422	+	1	NA	Intergenic	L1Md_T|LINE|L1	33852	NR_033535	100038734	Mm.387484	NR_033535	ENSMUSG00000095959	Gm10845	-	predicted gene 10845	ncRNA
Merged-chr12-113668489-1	chr12	113668388	113668590	+	1	NA	Intergenic	RLTR16C_MM|LTR|ERVK	124581	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr19-5474738-1	chr19	5474453	5475023	+	1	NA	promoter-TSS (NM_001164352)	promoter-TSS (NM_001164352)	3	NM_001164352	58859	Mm.276367	NM_021474	ENSMUSG00000024909	Efemp2	0610011K11Rik|Fbln4|MBP1	epidermal growth factor-containing fibulin-like extracellular matrix protein 2	protein-coding
Merged-chr14-51587882-1	chr14	51587786	51587978	+	1	NA	intron (NM_001013816, intron 1 of 4)	intron (NM_001013816, intron 1 of 4)	35092	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr13-62179088-1	chr13	62178985	62179191	+	1	NA	Intergenic	Intergenic	49198	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr1-114769307-1	chr1	114769224	114769391	+	1	NA	Intergenic	L1Md_T|LINE|L1	-915830	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr5-26032311-1	chr5	26032195	26032428	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	7194	NM_029376	75657	Mm.374273	NM_029376	ENSMUSG00000073119	Speer4a	1700027N01Rik|SPEER-4A	spermatogenesis associated glutamate (E)-rich protein 4A	protein-coding
Merged-chr6-136329800-1	chr6	136329678	136329923	+	1	NA	3' UTR (NM_001142734, exon 2 of 2)	3' UTR (NM_001142734, exon 2 of 2)	2261	NM_001142734	668137	Mm.417085	NM_001142734	ENSMUSG00000094973	Gm8994	B020013A22Rik|EG668137	predicted gene 8994	protein-coding
Merged-chr1-143864206-1	chr1	143864090	143864322	+	1	NA	Intergenic	L1Md_T|LINE|L1	86928	NM_019562	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
Merged-chr15-88836625-1	chr15	88836516	88836734	+	1	NA	Intergenic	Intergenic	16979	NM_029720	76737	Mm.292567	NM_029720	ENSMUSG00000023272	Creld2	5730592L21Rik|C85758	cysteine-rich with EGF-like domains 2	protein-coding
Merged-chr1-164737317-1	chr1	164737201	164737434	+	1	NA	Intergenic	L1Md_T|LINE|L1	-59346	NM_019759	56429	Mm.28935	NM_019759	ENSMUSG00000026574	Dpt	1810032B19Rik|5033416F05Rik|EQ-1|Eq1	dermatopontin	protein-coding
Merged-chrX-3086693-1	chrX	3086590	3086797	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	9773	NM_001270667	100861966	Mm.443264	NM_001270667	ENSMUSG00000100249	Btbd35f23	Gm21950|Mgclh	BTB domain containing 35, family member 23	protein-coding
Merged-chr12-115100842-1	chr12	115100746	115100938	+	1	NA	Intergenic	L1Md_T|LINE|L1	-587148	NR_106063	102465664		NR_106063	ENSMUSG00000098357	Mir7094-2	Gm27508|mmu-mir-7094-2	microRNA 7094-2	ncRNA
Merged-chr15-101931978-1	chr15	101931832	101932125	+	1	NA	intron (NM_146063, intron 4 of 8)	intron (NM_146063, intron 4 of 8)	-7243	NM_008475	16682	Mm.46425	NM_008475	ENSMUSG00000059668	Krt4	AW108092|K4|Krt-2.4|Krt2-4	keratin 4	protein-coding
Merged-chr11-52553931-1	chr11	52553809	52554053	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	157503	NM_153117	213673	Mm.291979	NM_153117	ENSMUSG00000036275	9530068E07Rik	C85061|Kct2	RIKEN cDNA 9530068E07 gene	protein-coding
Merged-chr1-33015159-1	chr1	33015051	33015267	+	1	NA	Intergenic	L1Md_T|LINE|L1	-467866	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr12-35908287-1	chr12	35908057	35908518	+	1	NA	Intergenic	L1Md_T|LINE|L1	-17334	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
Merged-chr6-64656643-1	chr6	64656427	64656859	+	1	NA	intron (NM_008167, intron 14 of 15)	ETnERV3-int|LTR|ERVK	-72482	NM_007500	11921	Mm.57229	NM_007500	ENSMUSG00000073043	Atoh1	Hath1|MATH-1|Math1|bHLHa14	atonal bHLH transcription factor 1	protein-coding
Merged-chr8-71172590-1	chr8	71172511	71172670	+	1	NA	intron (NR_131056, intron 2 of 4)	L1_Mus3|LINE|L1	32221	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
Merged-chr1-185160348-1	chr1	185160260	185160437	+	1	NA	Intergenic	L1Md_T|LINE|L1	-43820	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
Merged-chr7-10010478-1	chr7	10010255	10010702	+	1	NA	Intergenic	L1Md_A|LINE|L1	-18339	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr1-7192783-1	chr1	7192688	7192878	+	1	NA	Intergenic	L1Md_T|LINE|L1	103863	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
Merged-chr17-36029141-1	chr17	36028999	36029283	+	1	NA	TTS (NM_010398)	TTS (NM_010398)	3560	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
Merged-chr8-86288117-1	chr8	86288029	86288205	+	1	NA	Intergenic	MT2_Mm|LTR|ERVL	278473	NM_172912	244562	Mm.67485	NM_172912	ENSMUSG00000036872	Abcc12	4930467B22Rik|MRP9	ATP-binding cassette, sub-family C (CFTR/MRP), member 12	protein-coding
Merged-chr1-114178295-1	chr1	114178166	114178425	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1506842	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr8-127544480-1	chr8	127544381	127544580	+	1	NA	intron (NM_033620, intron 22 of 24)	(CA)n|Simple_repeat|Simple_repeat	244828	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
Merged-chr15-76188242-1	chr15	76188096	76188388	+	1	NA	exon (NM_201391, exon 17 of 32)	exon (NM_201391, exon 17 of 32)	7468	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr3-137659433-1	chr3	137659344	137659522	+	1	NA	Intergenic	L1Md_T|LINE|L1	35761	NM_030143	73284	Mm.250841	NM_030143	ENSMUSG00000046818	Ddit4l	1700037B15Rik|1700108M02Rik|REDD2|RTP801L|Smhs1	DNA-damage-inducible transcript 4-like	protein-coding
Merged-chr12-44233482-1	chr12	44233370	44233594	+	1	NA	Intergenic	L1Md_A|LINE|L1	12126	NR_045113	100039062	Mm.490648	NR_045113		Gm2027	-	nuclear assembly factor 1 homolog pseudogene	pseudo
Merged-chr11-8150765-1	chr11	8150669	8150861	+	1	NA	Intergenic	L1Md_T|LINE|L1	513770	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
Merged-chr1-109040282-1	chr1	109040191	109040374	+	1	NA	Intergenic	L1Md_T|LINE|L1	-942618	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr10-16693560-1	chr10	16693438	16693682	+	1	NA	Intergenic	L1Md_T|LINE|L1	402222	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr11-120251432-1	chr11	120251298	120251566	+	1	NA	intron (NM_198423, intron 2 of 27)	intron (NM_198423, intron 2 of 27)	18485	NM_198423	268515	Mm.309498	NM_198423	ENSMUSG00000039741	Bahcc1	B930044J06|BC060615	BAH domain and coiled-coil containing 1	protein-coding
Merged-chr19-6248049-1	chr19	6247964	6248134	+	1	NA	exon (NM_194348, exon 10 of 40)	exon (NM_194348, exon 10 of 40)	6381	NM_194348	329015	Mm.277384	NM_194348	ENSMUSG00000024773	Atg2a	1810013C15Rik|A830054M12|BC023754|mKIAA0404	autophagy related 2A	protein-coding
Merged-chr12-13423430-1	chr12	13423315	13423546	+	1	NA	intron (NM_027706, intron 35 of 51)	L1Md_T|LINE|L1	154303	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
Merged-chr13-93222553-1	chr13	93222462	93222645	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-30136	NM_133905	100715	Mm.242865	NM_133905	ENSMUSG00000042167	Papd4	8030446C20Rik|AI649009|GLD-2|Gld2	PAP associated domain containing 4	protein-coding
Merged-chr1-44478053-1	chr1	44477861	44478245	+	1	NA	Intergenic	L1Md_T|LINE|L1	-73618	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
Merged-chr7-10024946-1	chr7	10024844	10025048	+	1	NA	Intergenic	L1_Mus3|LINE|L1	28232	NM_001105178	434117	Mm.247383	NM_001105178	ENSMUSG00000094606	Vmn2r50	EG434117	vomeronasal 2, receptor 50	protein-coding
Merged-chr1-173893699-1	chr1	173893587	173893812	+	1	NA	Intergenic	L1Md_A|LINE|L1	-13512	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
Merged-chr17-27418560-1	chr17	27418473	27418648	+	1	NA	Intergenic	ORR1C2|LTR|ERVL-MaLR	60463	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr13-100444298-1	chr13	100444186	100444411	+	1	NA	exon (NM_008670, exon 3 of 16)	exon (NM_008670, exon 3 of 16)	8566	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
Merged-chr10-49279734-1	chr10	49279649	49279820	+	1	NA	intron (NM_001358866, intron 11 of 16)	L1Md_A|LINE|L1	508203	NM_001358866	14806	Mm.185993	NM_010349	ENSMUSG00000056073	Grik2	AW124492|C130030K03Rik|GluK2|Glur-6|Glur6|Glurbeta2	glutamate receptor, ionotropic, kainate 2 (beta 2)	protein-coding
Merged-chr1-31699679-1	chr1	31699559	31699800	+	1	NA	Intergenic	L1Md_T|LINE|L1	434832	NR_015347	226957	Mm.25966	NR_015347		Gm4850	EG226957	THO complex 4 pseudogene	pseudo
Merged-chr2-56801141-1	chr2	56801061	56801222	+	1	NA	Intergenic	L1Md_T|LINE|L1	15330	NR_105751	102465169		NR_105751	ENSMUSG00000098437	Mir195b	Gm27491|mmu-mir-195b	microRNA 195b	ncRNA
Merged-chr12-8909627-1	chr12	8909472	8909782	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-11680	NM_008640	17775	Mm.30071	NM_008640	ENSMUSG00000020585	Laptm4a	AA286466|LAPTM4|MTP|Mtrp|mKIAA0108	lysosomal-associated protein transmembrane 4A	protein-coding
Merged-chr1-34417927-1	chr1	34417793	34418062	+	1	NA	Intergenic	L1Md_T|LINE|L1	15272	NR_039562	100628580		NR_039562	ENSMUSG00000092852	Mir5103	mir-5103|mmu-mir-5103|mu-mir-5103	microRNA 5103	ncRNA
Merged-chr19-3970366-1	chr19	3970288	3970444	+	1	NA	TTS (NM_028545)	TTS (NM_028545)	-1962	NM_001177438	621603	Mm.34137	NM_001177438	ENSMUSG00000075296	Aldh3b2	AI848594|C130048D07Rik	aldehyde dehydrogenase 3 family, member B2	protein-coding
Merged-chr15-81310031-1	chr15	81309884	81310178	+	1	NA	Intergenic	Intergenic	50734	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
Merged-chr13-8813332-1	chr13	8813224	8813441	+	1	NA	intron (NM_001039388, intron 13 of 13)	L1Md_A|LINE|L1	57712	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
Merged-chr1-5434981-1	chr1	5434860	5435102	+	1	NA	Intergenic	L1Md_A|LINE|L1	-153512	NM_001318735	18387	Mm.7977	NM_011011	ENSMUSG00000025905	Oprk1	K-OR-1|KOR|KOR-1|MSL-1|Oprk2|R21	opioid receptor, kappa 1	protein-coding
Merged-chr11-114959447-1	chr11	114959348	114959547	+	1	NA	intron (NM_199225, intron 2 of 3)	intron (NM_199225, intron 2 of 3)	970	NM_199225	387565	Mm.351450	NM_199225	ENSMUSG00000058728	Cd300c	Clm6	CD300C molecule	protein-coding
Merged-chr15-91992214-1	chr15	91992039	91992390	+	1	NA	Intergenic	L1Md_A|LINE|L1	-58951	NM_001159648	12805	Mm.4911	NM_007727	ENSMUSG00000055022	Cntn1	AW495098|CNTN|F3cam|usl	contactin 1	protein-coding
Merged-chr15-33569588-1	chr15	33569492	33569684	+	1	NA	intron (NM_176073, intron 7 of 7)	L1Md_F2|LINE|L1	83848	NR_045070	75880	Mm.396109	NR_045070	ENSMUSG00000115779	4930592A05Rik	-	RIKEN cDNA 4930592A05 gene	ncRNA
Merged-chr15-58844204-1	chr15	58844085	58844324	+	1	NA	Intergenic	RMER17B2|LTR|ERVK	-20777	NM_175212	74868	Mm.293754	NM_175212	ENSMUSG00000062373	Tmem65	2610029O13Rik|4930438D12Rik	transmembrane protein 65	protein-coding
Merged-chr9-33041017-1	chr9	33040920	33041115	+	1	NA	Intergenic	L1Md_A|LINE|L1	-112051	NR_131058	330917	Mm.488283	NR_131058		Gm27162	A430016B06	predicted gene 27162	ncRNA
Merged-chr10-28043535-1	chr10	28043372	28043699	+	1	NA	Intergenic	L1Md_T|LINE|L1	-31285	NM_008983	19272	Mm.332303	NM_008983	ENSMUSG00000019889	Ptprk	AI853699|PTPk|RPTPkappa	protein tyrosine phosphatase, receptor type, K	protein-coding
Merged-chr1-109036424-1	chr1	109036323	109036526	+	1	NA	Intergenic	L1Md_T|LINE|L1	-946476	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr1-98646277-1	chr1	98646189	98646365	+	1	NA	Intergenic	L1Md_A|LINE|L1	225153	NM_001164233	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
Merged-chr13-65341784-1	chr13	65341540	65342029	+	1	NA	Intergenic	B3|SINE|B2	62930	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
Merged-chr11-113054988-1	chr11	113054858	113055118	+	1	NA	intron (NR_015556, intron 2 of 2)	L1Md_T|LINE|L1	146850	NR_015556	72386	Mm.266961	NR_015556	ENSMUSG00000087259	2610035D17Rik	-	RIKEN cDNA 2610035D17 gene	ncRNA
Merged-chr1-140710131-1	chr1	140710049	140710213	+	1	NA	Intergenic	L1Md_A|LINE|L1	-53729	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr1-48285380-1	chr1	48285265	48285496	+	1	NA	Intergenic	L1Md_T|LINE|L1	-818255	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr2-88247443-1	chr2	88247341	88247546	+	1	NA	Intergenic	L1Md_T|LINE|L1	-22413	NM_146532	258525	Mm.377552	NM_146532	ENSMUSG00000075133	Olfr1170	MOR174-12	olfactory receptor 1170	protein-coding
Merged-chr12-113659721-1	chr12	113659496	113659946	+	1	NA	Intergenic	Intergenic	115813	NM_174885	238406	Mm.188683	NM_174885	ENSMUSG00000043945	Adam6a	Adam6|tMDCIV	a disintegrin and metallopeptidase domain 6A	protein-coding
Merged-chr15-73090901-1	chr15	73090801	73091002	+	1	NA	intron (NM_053068, intron 1 of 2)	CpG	489	NM_053068	93696	Mm.23095	NM_053068	ENSMUSG00000068391	Chrac1	2410152E03Rik|2810406L04Rik|YCL1	chromatin accessibility complex 1	protein-coding
Merged-chr1-81423240-1	chr1	81423108	81423373	+	1	NA	Intergenic	L1Md_T|LINE|L1	345833	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
Merged-chr8-71145192-1	chr8	71145109	71145276	+	1	NA	intron (NM_001324526, intron 3 of 10)	Lx5|LINE|L1	4823	NM_001324526	665858	Mm.411658	NM_001324526		Gm7827	EG665858	predicted gene 7827	protein-coding
Merged-chr10-69231963-1	chr10	69231767	69232160	+	1	NA	intron (NM_001252638, intron 2 of 11)	L1Md_T|LINE|L1	18769	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
Merged-chr9-47494609-1	chr9	47494527	47494692	+	1	NA	Intergenic	L1Md_F3|LINE|L1	-35561	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
Merged-chr4-64990648-1	chr4	64990523	64990773	+	1	NA	Intergenic	L1Md_T|LINE|L1	-133526	NM_021362	18491	Mm.317854	NM_021362	ENSMUSG00000028370	Pappa	8430414N03Rik|IGFBP-4ase|PAG1|PAPP-A	pregnancy-associated plasma protein A	protein-coding
Merged-chr15-98977128-1	chr15	98977022	98977235	+	1	NA	Intergenic	Intergenic	-8837	NR_045991	75951	Mm.441657	NR_045991	ENSMUSG00000097587	4930578M01Rik	3010001K12Rik	RIKEN cDNA 4930578M01 gene	ncRNA
Merged-chr10-37731213-1	chr10	37731077	37731349	+	1	NA	Intergenic	L1Md_A|LINE|L1	-444561	NR_131035	75877	Mm.402094	NR_131035	ENSMUSG00000111234	4930591E09Rik	-	RIKEN cDNA 4930591E09 gene	ncRNA
Merged-chr17-34971868-1	chr17	34971776	34971961	+	1	NA	promoter-TSS (NM_013558)	promoter-TSS (NM_013558)	288	NM_010479	193740	Mm.6388	NM_010479	ENSMUSG00000091971	Hspa1a	Hsp70-3|Hsp70.3|Hsp72|hsp68|hsp70A1	heat shock protein 1A	protein-coding
Merged-chr17-16993077-1	chr17	16992960	16993194	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-71026	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr7-103961087-1	chr7	103960964	103961211	+	1	NA	Intergenic	L1Md_T|LINE|L1	14519	NM_146354	258351	Mm.377448	NM_146354	ENSMUSG00000073937	Olfr633	MOR12-5	olfactory receptor 633	protein-coding
Merged-chr8-3914501-1	chr8	3914420	3914582	+	1	NA	Intergenic	L1Md_T|LINE|L1	12340	NM_001037800	69165	Mm.175163	NM_026972	ENSMUSG00000065987	Cd209b	1810030I22Rik|DC-SIGNR1|OtB7|SIGNR1|mSIGNR1	CD209b antigen	protein-coding
Merged-chr17-26923322-1	chr17	26923179	26923466	+	1	NA	intron (NM_053173, intron 6 of 10)	intron (NM_053173, intron 6 of 10)	2360	NR_105933	102466211		NR_105933	ENSMUSG00000098586	Gm27775	Mir6967|Mir6967-1|mmu-mir-6967|mmu-mir-6967-1	predicted gene, 27775	ncRNA
Merged-chr10-74771939-1	chr10	74771720	74772159	+	1	NA	Intergenic	L1Md_A|LINE|L1	-195238	NM_010311	14687	Mm.32595	NM_010311	ENSMUSG00000040009	Gnaz	AI847979|Gz	guanine nucleotide binding protein, alpha z subunit	protein-coding
Merged-chr12-32537236-1	chr12	32537149	32537324	+	1	NA	Intergenic	L1Md_A|LINE|L1	158447	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
Merged-chr17-56420131-1	chr17	56420019	56420243	+	1	NA	intron (NM_001252455, intron 16 of 27)	(CGTG)n|Simple_repeat|Simple_repeat	-1222	NR_105943	102465590		NR_105943	ENSMUSG00000098339	Mir6977	Gm27922|mmu-mir-6977	microRNA 6977	ncRNA
Merged-chr15-8507209-1	chr15	8507093	8507325	+	1	NA	Intergenic	Intergenic	-62746	NM_027707	71175	Mm.240329	NM_027707	ENSMUSG00000022141	Nipbl	Idn3	NIPBL cohesin loading factor	protein-coding
Merged-chr15-73933800-1	chr15	73933695	73933905	+	1	NA	Intergenic	MER20|DNA|hAT-Charlie	-94129	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
Merged-chr1-91622270-1	chr1	91622157	91622384	+	1	NA	Intergenic	L1Md_T|LINE|L1	81190	NM_023046	65247	Mm.234152	NM_023046	ENSMUSG00000026311	Asb1	1700029O08Rik|1700054C17Rik|AI426616|AI851378|mKIAA1146	ankyrin repeat and SOCS box-containing 1	protein-coding
Merged-chrX-140896592-1	chrX	140896493	140896692	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-11016	NM_030181	78789	Mm.244932	NM_026103	ENSMUSG00000031430	Vsig1	1700062D20Rik|4930405J24Rik	V-set and immunoglobulin domain containing 1	protein-coding
Merged-chr13-68061823-1	chr13	68061669	68061978	+	1	NA	Intergenic	IAPEy-int|LTR|ERVK	169997	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr17-30772384-1	chr17	30772299	30772469	+	1	NA	intron (NM_013811, intron 66 of 92)	B3A|SINE|B2	-129483	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
Merged-chr13-3179830-1	chr13	3179671	3179989	+	1	NA	intron (NR_001581, intron 3 of 4)	RLTR6-int|LTR|ERV1	30355	NR_001581	73266	Mm.335891	NR_001581	ENSMUSG00000091304	Speer6-ps1	1700039A02Rik|Alb-cre|Alb<cre>|AlbCre|SPEER-6|Tg(Alb-cre)21Mgn|albumin-cre|cr<Alb>	spermatogenesis associated glutamate (E)-rich protein 6, pseudogene 1	pseudo
Merged-chr10-33825495-1	chr10	33825137	33825853	+	1	NA	Intergenic	L1Md_T|LINE|L1	-32227	NM_020565	57430	Mm.6590	NM_020565	ENSMUSG00000069668	Sult3a1	ST3A1|Sult-x2|Sultx2	sulfotransferase family 3A, member 1	protein-coding
Merged-chr4-88770238-1	chr4	88770131	88770345	+	1	NA	Intergenic	MMERVK10C-int|LTR|ERVK	-3596	NM_001243155	545646	Mm.380019	NM_001243155	ENSMUSG00000094271	Gm13290	-	predicted gene 13290	protein-coding
Merged-chr1-190455798-1	chr1	190455627	190455969	+	1	NA	Intergenic	L1Md_T|LINE|L1	52150	NR_151624	433390	Mm.331295	NR_151624	ENSMUSG00000103644	Gm29678	-	predicted gene, 29678	ncRNA
Merged-chr17-30836604-1	chr17	30836512	30836697	+	1	NA	intron (NM_013811, intron 87 of 92)	B3|SINE|B2	-65263	NM_021332	14652	Mm.390969	NM_021332	ENSMUSG00000024027	Glp1r	GLP-1R|GLP1Rc	glucagon-like peptide 1 receptor	protein-coding
Merged-chr11-45771530-1	chr11	45771367	45771694	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36553	NR_045876	100009664	Mm.415439	NR_045876		F630206G17Rik	-	RIKEN cDNA F630206G17 gene	ncRNA
Merged-chr1-121208167-1	chr1	121208026	121208308	+	1	NA	Intergenic	L1Md_A|LINE|L1	119511	NM_001271531	72999	Mm.27136	NM_133748	ENSMUSG00000003721	Insig2	2900053I11Rik|C730043J18Rik|Insig-2	insulin induced gene 2	protein-coding
Merged-chr13-66827194-1	chr13	66827057	66827331	+	1	NA	Intergenic	Intergenic	78156	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-89219330-1	chr1	89219226	89219435	+	1	NA	Intergenic	Intergenic	148915	NM_133816	98402	Mm.170983	NM_133816	ENSMUSG00000036206	Sh3bp4	AI594717|AW227605|BOG25	SH3-domain binding protein 4	protein-coding
Merged-chr1-36951798-1	chr1	36951712	36951885	+	1	NA	Intergenic	L1Md_T|LINE|L1	-12271	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
Merged-chr1-22154542-1	chr1	22154392	22154692	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-191892	NM_001310477	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
Merged-chr11-15303804-1	chr11	15303692	15303917	+	1	NA	Intergenic	L1Md_A|LINE|L1	704564	NM_001164166	432536	Mm.33646	NM_001164166	ENSMUSG00000084135	Pom121l12	1700054H16Rik	POM121 membrane glycoprotein-like 12	protein-coding
Merged-chr15-89167736-1	chr15	89167603	89167870	+	1	NA	exon (NM_138749, exon 4 of 38)	exon (NM_138749, exon 4 of 38)	-4828	NR_106066	102465672		NR_106066	ENSMUSG00000106328	Mir7118	mmu-mir-7118	microRNA 7118	ncRNA
Merged-chr19-5561030-1	chr19	5560949	5561112	+	1	NA	promoter-TSS (NM_019935)	promoter-TSS (NM_019935)	-455	NM_019935	18426	Mm.280225	NM_019935	ENSMUSG00000024922	Ovol1	BB147136|Ovo1|movo1	ovo like zinc finger 1	protein-coding
Merged-chr15-81811900-1	chr15	81811811	81811990	+	1	NA	intron (NM_017376, intron 1 of 3)	intron (NM_017376, intron 1 of 3)	486	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
Merged-chr12-26038915-1	chr12	26038815	26039015	+	1	NA	Intergenic	L1Md_A|LINE|L1	171590	NR_131149	629481	Mm.390460	NR_131149	ENSMUSG00000113550	Gm29687	-	predicted gene, 29687	ncRNA
Merged-chr18-3217163-1	chr18	3217057	3217269	+	1	NA	Intergenic	RLTR10|LTR|ERVK	63969	NM_001311066	12916	Mm.5244	NM_013498	ENSMUSG00000063889	Crem	ICER|ICERI	cAMP responsive element modulator	protein-coding
Merged-chr15-7028639-1	chr15	7028554	7028725	+	1	NA	Intergenic	(GA)n|Simple_repeat|Simple_repeat	-100933	NM_001113386	16880	Mm.149720	NM_013584	ENSMUSG00000054263	Lifr	A230075M04Rik|AW061234|LIF	leukemia inhibitory factor receptor	protein-coding
Merged-chr11-18516882-1	chr11	18516788	18516977	+	1	NA	Intergenic	L1Md_A|LINE|L1	420896	NR_131129	327872		NR_131129	ENSMUSG00000085453	Gm12018	-	predicted gene 12018	ncRNA
Merged-chr1-81499654-1	chr1	81499563	81499746	+	1	NA	Intergenic	L1_Mm|LINE|L1	422247	NM_001356397	241134	Mm.313904	NM_172849	ENSMUSG00000054976	Nyap2	9430031J16Rik|Jr6|Kiaa1486	neuronal tyrosine-phophorylated phosphoinositide 3-kinase adaptor 2	protein-coding
Merged-chr19-5089547-1	chr19	5089447	5089647	+	1	NA	exon (NM_026553, exon 2 of 8)	exon (NM_026553, exon 2 of 8)	1009	NM_026553	68090	Mm.44202	NM_026553	ENSMUSG00000024875	Yif1a	5330422J23Rik|54TM|Yif1|Yif1p	Yip1 interacting factor homolog A (S. cerevisiae)	protein-coding
Merged-chr11-89558922-1	chr11	89558828	89559016	+	1	NA	intron (NM_001327810, intron 2 of 19)	L1Md_A|LINE|L1	138014	NM_001327810	382543	Mm.60997	NM_172534	ENSMUSG00000047773	Ankfn1	4932411E22Rik|Gm1175|nmf9	ankyrin-repeat and fibronectin type III domain containing 1	protein-coding
Merged-chr1-45168718-1	chr1	45168631	45168805	+	1	NA	Intergenic	L1Md_A|LINE|L1	-142820	NM_009930	12825	Mm.249555	NM_009930	ENSMUSG00000026043	Col3a1	AW550625|Col3a-1|Tsk-2|Tsk2	collagen, type III, alpha 1	protein-coding
Merged-chr15-59638565-1	chr15	59638476	59638654	+	1	NA	Intergenic	Intergenic	-10089	NM_144549	211770	Mm.40298	NM_144549	ENSMUSG00000032501	Trib1	A530090O15Rik|TRB-1|Trb1	tribbles pseudokinase 1	protein-coding
Merged-chr17-17221577-1	chr17	17221424	17221731	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-13326	NM_001362181	102640673		NM_001362181		LOC102640673	-	zinc finger protein 431-like	protein-coding
Merged-chr17-17015498-1	chr17	17015418	17015578	+	1	NA	Intergenic	L1Md_A|LINE|L1	-48605	NM_001005358	449000	Mm.483718	NM_001005358	ENSMUSG00000096696	Zfp960	-	zinc finger protein 960	protein-coding
Merged-chr12-14451344-1	chr12	14451126	14451563	+	1	NA	Intergenic	L1Md_T|LINE|L1	189810	NR_045003	791361	Mm.217963	NR_045003	ENSMUSG00000113336	Gm16497	-	predicted gene 16497	ncRNA
Merged-chr1-16071729-1	chr1	16071555	16071903	+	1	NA	intron (NM_001305227, intron 4 of 5)	intron (NM_001305227, intron 4 of 5)	21596	NM_001305227	75799	Mm.78557	NM_001243238	ENSMUSG00000067795	4930444P10Rik	-	RIKEN cDNA 4930444P10 gene	protein-coding
Merged-chr19-8391694-1	chr19	8391503	8391885	+	1	NA	intron (NM_177002, intron 2 of 9)	ERVB4_1B-I_MM-int|LTR|ERVK	13411	NM_177002	319800	Mm.426083	NM_177002	ENSMUSG00000052562	Slc22a30	AA986766|C730048C13Rik|UST1R	solute carrier family 22, member 30	protein-coding
Merged-chr12-10914887-1	chr12	10914742	10915032	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132926	NR_045860	71457	Mm.95280	NR_045860	ENSMUSG00000113620	7420701I03Rik	-	RIKEN cDNA 7420701I03 gene	ncRNA
Merged-chr19-57144041-1	chr19	57143951	57144132	+	1	NA	intron (NM_001103177, intron 4 of 21)	B1_Mus1|SINE|Alu	-25017	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
Merged-chr17-40984987-1	chr17	40984886	40985088	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	50302	NM_008650	17850	Mm.259884	NM_008650	ENSMUSG00000023921	Mut	D230010K02Rik|Mcm	methylmalonyl-Coenzyme A mutase	protein-coding
Merged-chr5-84376320-1	chr5	84376225	84376416	+	1	NA	intron (NM_007937, intron 2 of 15)	L1Md_T|LINE|L1	41062	NM_007937	13839	Mm.137991	NM_007937	ENSMUSG00000029245	Epha5	AI854630|AW125296|Cek7|Ehk1|Els1|Hek7|Rek7|bsk	Eph receptor A5	protein-coding
Merged-chr6-116552120-1	chr6	116551943	116552298	+	1	NA	Intergenic	Intergenic	-4307	NM_146759	258754	Mm.451661	NM_146759	ENSMUSG00000051046	Olfr214	MOR119-1	olfactory receptor 214	protein-coding
Merged-chr12-69022625-1	chr12	69022536	69022714	+	1	NA	Intergenic	L1Md_T|LINE|L1	136561	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr19-46482227-1	chr19	46482120	46482335	+	1	NA	intron (NM_001025391, intron 10 of 11)	intron (NM_001025391, intron 10 of 11)	-19421	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
Merged-chr15-81811527-1	chr15	81811423	81811632	+	1	NA	5' UTR (NM_017376, exon 1 of 4)	5' UTR (NM_017376, exon 1 of 4)	113	NM_017376	21685	Mm.270278	NM_017376	ENSMUSG00000022389	Tef	2310028D20Rik	thyrotroph embryonic factor	protein-coding
Merged-chr15-89225637-1	chr15	89225558	89225717	+	1	NA	intron (NM_026813, intron 1 of 24)	intron (NM_026813, intron 1 of 24)	14078	NM_001356969	71474	Mm.184055	NM_026813	ENSMUSG00000036561	Ppp6r2	1110033O10Rik|8430411H09Rik|B230107H12Rik|Pp6r2|Saps2	protein phosphatase 6, regulatory subunit 2	protein-coding
Merged-chr1-19377492-1	chr1	19377384	19377601	+	1	NA	Intergenic	L1Md_T|LINE|L1	165438	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr17-21122403-1	chr17	21122239	21122568	+	1	NA	Intergenic	Intergenic	31195	NR_137274	328766	Mm.50947	NR_137274	ENSMUSG00000102080	Gm5092	4933430A09	predicted gene 5092	ncRNA
Merged-chr19-7152153-1	chr19	7152062	7152245	+	1	NA	intron (NM_134147, intron 3 of 10)	intron (NM_134147, intron 3 of 10)	-46424	NM_201411	396184	Mm.386930	NM_201411	ENSMUSG00000047787	Flrt1	AW742165|D630040I23Rik	fibronectin leucine rich transmembrane protein 1	protein-coding
Merged-chr19-5024162-1	chr19	5024015	5024309	+	1	NA	5' UTR (NM_007854, exon 1 of 12)	5' UTR (NM_007854, exon 1 of 12)	156	NM_007854	13340	Mm.4930	NM_007854	ENSMUSG00000024891	Slc29a2	Der12|Ent2|Hnp36	solute carrier family 29 (nucleoside transporters), member 2	protein-coding
Merged-chr1-25126038-1	chr1	25125905	25126171	+	1	NA	intron (NM_175642, intron 22 of 30)	L1Md_T|LINE|L1	151916	NM_001204913	100504323	Mm.484176	NM_001204913		Gm20172	-	predicted gene, 20172	protein-coding
Merged-chr5-26090053-1	chr5	26089964	26090142	+	1	NA	promoter-TSS (NM_001177579)	promoter-TSS (NM_001177579)	-789	NM_001177579	100039045	Mm.375471	NM_001177579	ENSMUSG00000073116	Gm10471	-	predicted gene 10471	protein-coding
Merged-chr8-36613664-1	chr8	36613569	36613760	+	1	NA	5' UTR (NM_015802, exon 1 of 14)	5' UTR (NM_015802, exon 1 of 14)	279	NM_015802	50768	Mm.125155	NM_015802	ENSMUSG00000031523	Dlc1	A730069N07Rik|Arhgap7|HP|STARD12|dlc-1	deleted in liver cancer 1	protein-coding
Merged-chr10-68519603-1	chr10	68519510	68519696	+	1	NA	intron (NM_028491, intron 3 of 7)	L1Md_T|LINE|L1	22272	NM_028491	73287	Mm.141830	NM_028491	ENSMUSG00000019945	Cabcoco1	1700040L02Rik	ciliary associated calcium binding coiled-coil 1	protein-coding
Merged-chr1-118586445-1	chr1	118586344	118586546	+	1	NA	intron (NM_001359330, intron 36 of 39)	L1Md_A|LINE|L1	-41500	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
Merged-chr1-79386157-1	chr1	79386066	79386249	+	1	NA	Intergenic	L1Md_T|LINE|L1	53933	NM_001310680	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
Merged-chr11-17581447-1	chr11	17581357	17581538	+	1	NA	Intergenic	L1Md_A|LINE|L1	323759	NM_001330649	57316	Mm.287982	NM_020558	ENSMUSG00000000581	C1d	1110036E10Rik|AI875855|SUN-CoR	C1D nuclear receptor co-repressor	protein-coding
Merged-chr11-44584711-1	chr11	44584581	44584841	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1606	NR_126460	75389	Mm.261421	NR_126460	ENSMUSG00000086501	4930597A21Rik	-	RIKEN cDNA 4930597A21 gene	ncRNA
Merged-chr15-79826843-1	chr15	79826711	79826975	+	1	NA	3' UTR (NM_028763, exon 5 of 5)	3' UTR (NM_028763, exon 5 of 5)	7490	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
Merged-chr7-8426739-1	chr7	8426642	8426837	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-43501	NM_001105074	434113	Mm.469891	NM_001105074	ENSMUSG00000094098	Vmn2r44	EG434113	vomeronasal 2, receptor 44	protein-coding
Merged-chrX-115388467-1	chrX	115388356	115388578	+	1	NA	Intergenic	L1Md_A|LINE|L1	461478	NR_130989	78086		NR_130989	ENSMUSG00000085619	4930555B12Rik	-	RIKEN cDNA 4930555B12 gene	ncRNA
Merged-chr1-125142178-1	chr1	125142096	125142260	+	1	NA	Intergenic	L1Md_T|LINE|L1	293549	NM_023735	74117	Mm.183102	NM_023735	ENSMUSG00000026341	Actr3	1200003A09Rik|Arp3	ARP3 actin-related protein 3	protein-coding
Merged-chr17-54050018-1	chr17	54049936	54050100	+	1	NA	Intergenic	L1Md_T|LINE|L1	-59387	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
Merged-chr1-148221526-1	chr1	148221435	148221617	+	1	NA	Intergenic	L1Md_A|LINE|L1	1700913	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr1-120997069-1	chr1	120996913	120997226	+	1	NA	Intergenic	L1Md_T|LINE|L1	-90336	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
Merged-chr13-66392499-1	chr13	66392364	66392635	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	48619	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-122109590-1	chr10	122109495	122109685	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10107	NR_027637	100043513	Mm.429141	NR_027637	ENSMUSG00000111952	Gm4489	Gm241	predicted gene 4489	ncRNA
Merged-chr1-93894775-1	chr1	93894648	93894902	+	1	NA	Intergenic	L1Md_T|LINE|L1	-23662	NM_001205249	100041596	Mm.417228	NM_001205249	ENSMUSG00000093805	Gal3st2b	Gal3ST-2|Gal3st2|Gm9994	galactose-3-O-sulfotransferase 2B	protein-coding
Merged-chr13-66264986-1	chr13	66264789	66265183	+	1	NA	Intergenic	Intergenic	151533	NM_001177832	628709	Mm.390595	NM_001177832	ENSMUSG00000095909	Gm10324	-	predicted gene 10324	protein-coding
Merged-chr17-23359386-1	chr17	23359226	23359546	+	1	NA	exon (NM_001104579, exon 6 of 6)	exon (NM_001104579, exon 6 of 6)	15409	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr1-21197771-1	chr1	21197399	21198143	+	1	NA	Intergenic	L1Md_T|LINE|L1	-20804	NM_001290679	75712	Mm.304763	NM_029398	ENSMUSG00000025933	Tmem14a	5730496E24Rik|C85783|PTD011	transmembrane protein 14A	protein-coding
Merged-chr12-30683102-1	chr12	30682991	30683213	+	1	NA	Intergenic	L1Md_T|LINE|L1	98659	NM_172049	211986	Mm.34035	NM_172049	ENSMUSG00000043061	Tmem18	BC024093	transmembrane protein 18	protein-coding
Merged-chr8-98939939-1	chr8	98939815	98940064	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-71948	NR_110579	100873092	Mm.414599	NR_110579	ENSMUSG00000089819	Gm15679	-	predicted gene 15679	ncRNA
Merged-chr17-25859594-1	chr17	25859514	25859675	+	1	NA	intron (NM_001163766, intron 6 of 40)	intron (NM_001163766, intron 6 of 40)	1921	NM_001163766	106618	Mm.35470	NM_134124	ENSMUSG00000073434	Wdr90	3230401M21Rik|AI551153|mKIAA1924	WD repeat domain 90	protein-coding
Merged-chr11-90581485-1	chr11	90581296	90581674	+	1	NA	intron (NM_011505, intron 10 of 17)	L1Md_T|LINE|L1	56623	NM_011505	20913	Mm.207203	NM_011505	ENSMUSG00000020546	Stxbp4	6030470M02Rik|Synip	syntaxin binding protein 4	protein-coding
Merged-chr11-38904127-1	chr11	38903854	38904400	+	1	NA	Intergenic	L1Md_A|LINE|L1	-384082	NR_040295	100502917	Mm.61144	NR_040295		Gm12130	-	predicted gene 12130	ncRNA
Merged-chr17-36138919-1	chr17	36138693	36139146	+	1	NA	Intergenic	Intergenic	-6099	NR_033517	675325	Mm.75890	NR_033517	ENSMUSG00000038311	2410017I17Rik	-	RIKEN cDNA 2410017I17 gene	ncRNA
Merged-chr5-146160669-1	chr5	146160588	146160750	+	1	NA	Intergenic	Intergenic	24635	NM_001008547	69282	Mm.373573	NM_001008547	ENSMUSG00000095040	1700001J03Rik	-	RIKEN cDNA 1700001J03 gene	protein-coding
Merged-chr13-61756461-1	chr13	61756348	61756575	+	1	NA	Intergenic	Lx3_Mus|LINE|L1	-15119	NR_028430	432812	Mm.317358	NR_028430		BC052688	-	cDNA sequence BC052688	pseudo
Merged-chr10-69230815-1	chr10	69230664	69230966	+	1	NA	intron (NM_001252638, intron 2 of 11)	L1Md_T|LINE|L1	17621	NM_001252638	69288	Mm.26659	NM_001081347	ENSMUSG00000019944	Rhobtb1	1700008H16Rik|3110048G13Rik|AI173445|AI573858|AV350930	Rho-related BTB domain containing 1	protein-coding
Merged-chr1-23300462-1	chr1	23300333	23300591	+	1	NA	Intergenic	L1Md_T|LINE|L1	8761	NR_029717	723964		NR_029717	ENSMUSG00000065567	Mir30c-2	Mirn30c-2|mir-30c-2	microRNA 30c-2	ncRNA
Merged-chr12-58126151-1	chr12	58126058	58126245	+	1	NA	Intergenic	L1Md_A|LINE|L1	-85653	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
Merged-chr8-128746837-1	chr8	128746691	128746984	+	1	NA	Intergenic	MMETn-int|LTR|ERVK	61183	NM_010578	16412	Mm.263396	NM_010578	ENSMUSG00000025809	Itgb1	4633401G24Rik|AA409975|AA960159|CD29|Fnrb|Gm9863|gpIIa	integrin beta 1 (fibronectin receptor beta)	protein-coding
Merged-chr1-22056886-1	chr1	22056756	22057017	+	1	NA	Intergenic	L1Md_A|LINE|L1	-94236	NM_001310477	226922	Mm.336519	NM_023872	ENSMUSG00000028033	Kcnq5	7730402H11|9230107O05Rik|AA589396|D1Mgi1	potassium voltage-gated channel, subfamily Q, member 5	protein-coding
Merged-chr15-74080498-1	chr15	74080411	74080586	+	1	NA	Intergenic	Intergenic	-240827	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
Merged-chr1-171575344-1	chr1	171575187	171575502	+	1	NA	intron (NM_018729, intron 3 of 8)	intron (NM_018729, intron 3 of 8)	16151	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
Merged-chr13-66655179-1	chr13	66655073	66655285	+	1	NA	Intergenic	L1Md_T|LINE|L1	-214061	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-97421824-1	chr1	97421711	97421938	+	1	NA	Intergenic	L1Md_T|LINE|L1	239852	NM_001355073	52392	Mm.12309	NM_133825	ENSMUSG00000044768	D1Ertd622e	AI987691|AW047450	DNA segment, Chr 1, ERATO Doi 622, expressed	protein-coding
Merged-chr15-63998170-1	chr15	63998091	63998249	+	1	NA	promoter-TSS (NM_001360035)	promoter-TSS (NM_001360035)	-104	NM_001360035	223601	Mm.246108	NM_144846	ENSMUSG00000022378	Fam49b	0910001A06Rik|AW122079	family with sequence similarity 49, member B	protein-coding
Merged-chr15-102112990-1	chr15	102112906	102113074	+	1	NA	exon (NM_153533, exon 20 of 29)	exon (NM_153533, exon 20 of 29)	10056	NM_001355636	209039	Mm.29389	NM_153533	ENSMUSG00000037003	Tns2	C1-ten|Tenc1|nep|nph	tensin 2	protein-coding
Merged-chr1-158884641-1	chr1	158884528	158884754	+	1	NA	intron (NM_001085376, intron 2 of 21)	L1Md_T|LINE|L1	72797	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
Merged-chr10-26168956-1	chr10	26168835	26169078	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-60751	NM_001013766	268288	Mm.213322	NM_001013766	ENSMUSG00000051354	Samd3	Gm623	sterile alpha motif domain containing 3	protein-coding
Merged-chr1-24642255-1	chr1	24642171	24642339	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36289	NM_026719	68421	Mm.336563	NM_026719	ENSMUSG00000073725	Lmbrd1	0910001K20Rik|AV347960	LMBR1 domain containing 1	protein-coding
Merged-chr10-47443424-1	chr10	47443231	47443618	+	1	NA	Intergenic	L1Md_T|LINE|L1	1198675	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr13-68082584-1	chr13	68082483	68082686	+	1	NA	Intergenic	ORR1A2|LTR|ERVL-MaLR	149236	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr5-85265210-1	chr5	85265091	85265330	+	1	NA	Intergenic	L1Md_T|LINE|L1	800373	NM_007683	12617	Mm.4649	NM_007683	ENSMUSG00000029253	Cenpc1	CENP-C|Cenpc	centromere protein C1	protein-coding
Merged-chr10-81057252-1	chr10	81057147	81057357	+	1	NA	intron (NM_001358550, intron 1 of 11)	intron (NM_001358550, intron 1 of 11)	2924	NM_001358549	52551	Mm.30068	NM_024499	ENSMUSG00000004937	Sgta	5330427H01Rik|AI194281|D10Ertd190e|Sgt|Stg	small glutamine-rich tetratricopeptide repeat (TPR)-containing, alpha	protein-coding
Merged-chr13-23411706-1	chr13	23411509	23411903	+	1	NA	Intergenic	Intergenic	12160	NM_013924	30946	Mm.292094	NM_013924	ENSMUSG00000036376	Abt1	-	activator of basal transcription 1	protein-coding
Merged-chr1-186106267-1	chr1	186106165	186106369	+	1	NA	intron (NM_146106, intron 2 of 4)	L1Md_T|LINE|L1	11043	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
Merged-chr10-110016283-1	chr10	110016183	110016383	+	1	NA	Intergenic	L1Md_A|LINE|L1	-16064	NM_001081035	260315	Mm.225050	NM_177797	ENSMUSG00000020181	Nav3	4732483H20Rik|9630020C08Rik|POMFIL1|Pomfil1p|mKIAA0938|unc53H3	neuron navigator 3	protein-coding
Merged-chr1-13735672-1	chr1	13735515	13735830	+	1	NA	Intergenic	L1Md_T|LINE|L1	51257	NR_004447	433273	Mm.304088	NR_004447	ENSMUSG00000097711	Gm5523	EG433273	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr15-98567410-1	chr15	98567295	98567526	+	1	NA	promoter-TSS (NR_028442)	promoter-TSS (NR_028442)	86	NR_028442	100048895	Mm.471074	NR_028442		9330020H09Rik	-	RIKEN cDNA 9330020H09 gene	ncRNA
Merged-chr1-17385255-1	chr1	17385152	17385359	+	1	NA	Intergenic	L1Md_T|LINE|L1	-216646	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
Merged-chr13-68063020-1	chr13	68062765	68063276	+	1	NA	Intergenic	IAPEy-int|LTR|ERVK	168800	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr11-40418344-1	chr11	40418236	40418452	+	1	NA	Intergenic	L1Md_T|LINE|L1	274338	NM_134017	108645	Mm.293771	NM_134017	ENSMUSG00000042032	Mat2b	1110064C04Rik|2410018D16Rik|AI182287|AU022853|MAT-II|MATIIbeta|TGR	methionine adenosyltransferase II, beta	protein-coding
Merged-chr19-46386115-1	chr19	46386000	46386231	+	1	NA	intron (NM_016860, intron 2 of 10)	intron (NM_016860, intron 2 of 10)	9620	NM_016860	54130	Mm.3118	NM_016860	ENSMUSG00000025228	Actr1a	Arp1|alpha-Arp1	ARP1 actin-related protein 1A, centractin alpha	protein-coding
Merged-chr1-99189396-1	chr1	99189280	99189512	+	1	NA	Intergenic	L1Md_A|LINE|L1	-583369	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr11-79236648-1	chr11	79236518	79236779	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	6376	NM_001042565	78889	Mm.307022	NM_019653	ENSMUSG00000017677	Wsb1	1110056B13Rik|2700038M07Rik	WD repeat and SOCS box-containing 1	protein-coding
Merged-chr6-116550646-1	chr6	116550553	116550739	+	1	NA	Intergenic	Lx2|LINE|L1	-5781	NM_146759	258754	Mm.451661	NM_146759	ENSMUSG00000051046	Olfr214	MOR119-1	olfactory receptor 214	protein-coding
Merged-chr15-88805331-1	chr15	88805202	88805461	+	1	NA	TTS (NM_145477)	TTS (NM_145477)	13987	NM_001142357	223774	Mm.41512	NM_145477	ENSMUSG00000035845	Alg12	ECM39	asparagine-linked glycosylation 12 (alpha-1,6-mannosyltransferase)	protein-coding
Merged-chr1-98648135-1	chr1	98647974	98648296	+	1	NA	Intergenic	L1Md_A|LINE|L1	227011	NM_001164233	70866	Mm.389164	NM_027584	ENSMUSG00000026336	Slco6d1	4921511I05Rik	solute carrier organic anion transporter family, member 6d1	protein-coding
Merged-chr13-66520558-1	chr13	66520470	66520646	+	1	NA	Intergenic	Intergenic	-79440	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-97670115-1	chr15	97670010	97670220	+	1	NA	Intergenic	Intergenic	35707	NM_028003	71919	Mm.12255	NM_028003	ENSMUSG00000022466	Rpap3	2310042P20Rik|D15Ertd682e	RNA polymerase II associated protein 3	protein-coding
Merged-chr6-32036586-1	chr6	32036422	32036750	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-13702	NM_029587	76382	Mm.23510	NM_029587	ENSMUSG00000029766	1700012A03Rik	AI429084	RIKEN cDNA 1700012A03 gene	protein-coding
Merged-chr1-99186162-1	chr1	99185948	99186377	+	1	NA	Intergenic	L1Md_A|LINE|L1	-586603	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr12-115150044-1	chr12	115149931	115150157	+	1	NA	Intergenic	Intergenic	545750	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-193072016-1	chr1	193071900	193072132	+	1	NA	Intergenic	L1Md_T|LINE|L1	-36241	NM_001301370	329324	Mm.76710	NM_181546	ENSMUSG00000016200	Syt14	B230320I09Rik|sytXIV	synaptotagmin XIV	protein-coding
Merged-chr12-101136847-1	chr12	101136753	101136941	+	1	NA	Intergenic	L1Md_T|LINE|L1	-8762	NR_033653	74947	Mm.488905	NR_033653	ENSMUSG00000092054	Kif4-ps	4930463M05Rik|Kif4b	kinesin family member 4, pseudogene	pseudo
Merged-chr19-57880292-1	chr19	57880114	57880471	+	1	NA	intron (NM_181415, intron 26 of 28)	intron (NM_181415, intron 26 of 28)	-170875	NR_049196	100885835		NR_049196	ENSMUSG00000093757	Mir5623	Gm26068|mir-5623|mmu-mir-5623	microRNA 5623	ncRNA
Merged-chr12-94851678-1	chr12	94851599	94851757	+	1	NA	Intergenic	L1Md_T|LINE|L1	-840548	NM_201518	399558	Mm.341948	NM_201518	ENSMUSG00000047414	Flrt2	-	fibronectin leucine rich transmembrane protein 2	protein-coding
Merged-chr13-62393696-1	chr13	62393512	62393881	+	1	NA	Intergenic	Intergenic	-10522	NM_001162910	100041979	Mm.445930	NM_001162910	ENSMUSG00000094942	Gm3604	-	predicted gene 3604	protein-coding
Merged-chr19-5833466-1	chr19	5833370	5833563	+	1	NA	non-coding (NR_131212, exon 1 of 1)	non-coding (NR_131212, exon 1 of 1)	12012	NR_131212	66961	Mm.281895	NR_003513	ENSMUSG00000092274	Neat1	2310043N10Rik|VINC	nuclear paraspeckle assembly transcript 1 (non-protein coding)	ncRNA
Merged-chr1-19374090-1	chr1	19373870	19374311	+	1	NA	Intergenic	L1Md_T|LINE|L1	162036	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr13-68054343-1	chr13	68054248	68054438	+	1	NA	Intergenic	Intergenic	177477	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr11-75660669-1	chr11	75660170	75661168	+	1	NA	intron (NM_001080774, intron 7 of 31)	B1_Mus1|SINE|Alu	4654	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
Merged-chr15-78736827-1	chr15	78736662	78736993	+	1	NA	Intergenic	Intergenic	-18056	NM_001358692	207393	Mm.323188	NM_183141	ENSMUSG00000043460	Elfn2	6330514E13|AW048948|BC094219|Lrrc62|Ppp1r29	leucine rich repeat and fibronectin type III, extracellular 2	protein-coding
Merged-chr15-35635181-1	chr15	35635097	35635265	+	1	NA	intron (NM_177151, intron 25 of 61)	L1Md_T|LINE|L1	25737	NR_035527	100316736		NR_035527	ENSMUSG00000076333	Mir599	mmu-mir-599	microRNA 599	ncRNA
Merged-chr19-59458355-1	chr19	59458263	59458447	+	1	NA	promoter-TSS (NM_010132)	promoter-TSS (NM_010132)	280	NR_002863	329078	Mm.80382	NR_002863	ENSMUSG00000087095	Emx2os	-	Emx2 opposite strand/antisense transcript (non-protein coding)	ncRNA
Merged-chr15-99537796-1	chr15	99537707	99537886	+	1	NA	Intergenic	IMPB_01|Satellite|Satellite	-9631	NM_028224	72393	Mm.39760	NM_028224	ENSMUSG00000023011	Faim2	2900002L20Rik|Lfg|Lfg2|NMP25|Nmp35|Tmbim2	Fas apoptotic inhibitory molecule 2	protein-coding
Merged-chr15-34678579-1	chr15	34678442	34678716	+	1	NA	exon (NM_145469, exon 1 of 11)	exon (NM_145469, exon 1 of 11)	127	NM_145469	223473	Mm.258402	NM_145469	ENSMUSG00000038879	Nipal2	9330161F08Rik|Npal2	NIPA-like domain containing 2	protein-coding
Merged-chr13-66635547-1	chr13	66635441	66635653	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	-194429	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-55635816-1	chr10	55635710	55635922	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-471101	NM_001163833	73390	Mm.181475	NM_133751	ENSMUSG00000047669	Msl3l2	1700060H10Rik	MSL3 like 2	protein-coding
Merged-chr5-29041461-1	chr5	29041357	29041565	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-154532	NM_001289757	56874	Mm.87352	NM_021470	ENSMUSG00000029130	Rnf32	1700009J01Rik|2700025B22Rik|4930542N22Rik|Lmbr2	ring finger protein 32	protein-coding
Merged-chr10-80381791-1	chr10	80381706	80381877	+	1	NA	exon (NM_198615, exon 2 of 2)	exon (NM_198615, exon 2 of 2)	5860	NM_198615	237400	Mm.268389	NM_198615	ENSMUSG00000048696	Mex3d	BC059858|Rkhd1	mex3 RNA binding family member D	protein-coding
Merged-chr16-64806760-1	chr16	64806640	64806881	+	1	NA	intron (NM_001347245, intron 3 of 8)	L1Md_A|LINE|L1	-20439	NM_028059	72020	Mm.25960	NM_028059	ENSMUSG00000047141	Zfp654	1600021C16Rik|1810008K20Rik|433036|Gm5488|Znf654	zinc finger protein 654	protein-coding
Merged-chr4-62499389-1	chr4	62499193	62499585	+	1	NA	exon (NM_024257, exon 2 of 2)	exon (NM_024257, exon 2 of 2)	2811	NM_024257	72748	Mm.41506	NM_024257	ENSMUSG00000038422	Hdhd3	2810435D12Rik	haloacid dehalogenase-like hydrolase domain containing 3	protein-coding
Merged-chr10-99071259-1	chr10	99071105	99071414	+	1	NA	Intergenic	L1Md_T|LINE|L1	-35823	NM_027740	382406	Mm.440656	NM_027740	ENSMUSG00000019952	Poc1b	4933430F16Rik|Wdr51b	POC1 centriolar protein B	protein-coding
Merged-chr11-37636868-1	chr11	37636693	37637043	+	1	NA	Intergenic	L1Md_A|LINE|L1	-22121	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr10-22592159-1	chr10	22592036	22592283	+	1	NA	Intergenic	Intergenic	-52852	NM_178934	353169	Mm.473705	NM_178934	ENSMUSG00000037490	Slc2a12	GLUT-12|Glut12	solute carrier family 2 (facilitated glucose transporter), member 12	protein-coding
Merged-chr12-91169340-1	chr12	91169258	91169423	+	1	NA	intron (NM_181815, intron 20 of 25)	L1Md_A|LINE|L1	59111	NR_030473	735273		NR_030473	ENSMUSG00000076118	Mir669c	Mirn669c|Mirn669c-1	microRNA 669c	ncRNA
Merged-chr13-66793511-1	chr13	66793302	66793720	+	1	NA	Intergenic	MMSAT4|Satellite|Satellite	111839	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-189448488-1	chr1	189448380	189448597	+	1	NA	Intergenic	L1Md_A|LINE|L1	-46215	NM_001281848	16526	Mm.33304	NM_010607	ENSMUSG00000037624	Kcnk2	A430027H14Rik|AI848635|TREK-1	potassium channel, subfamily K, member 2	protein-coding
Merged-chr5-137046266-1	chr5	137046186	137046347	+	1	NA	promoter-TSS (NM_007457)	promoter-TSS (NM_007457)	-158	NM_007457	11769	Mm.833	NM_007457	ENSMUSG00000004849	Ap1s1	AP19	adaptor protein complex AP-1, sigma 1	protein-coding
Merged-chr10-72013007-1	chr10	72012921	72013093	+	1	NA	Intergenic	L1Md_A|LINE|L1	-32317	NR_003644	108950	Mm.212793	NM_175390		1700049L16Rik	-	hematological and neurological expressed 1-like pseudogene	pseudo
Merged-chr1-84706690-1	chr1	84706597	84706783	+	1	NA	Intergenic	L1Md_A|LINE|L1	-10469	NM_152915	227325	Mm.292560	NM_152915	ENSMUSG00000036766	Dner	A930026D19Rik|BET|Bret	delta/notch-like EGF repeat containing	protein-coding
Merged-chr8-21011629-1	chr8	21011548	21011711	+	1	NA	Intergenic	Intergenic	-13916	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr14-17820631-1	chr14	17820490	17820772	+	1	NA	intron (NM_001113417, intron 1 of 9)	L1Md_A|LINE|L1	159671	NM_001113417	21834	Mm.32563	NM_009380	ENSMUSG00000021779	Thrb	Nr1a2|T3R[b]|T3Rbeta|Thrb1|Thrb2|c-erbAbeta	thyroid hormone receptor beta	protein-coding
Merged-chr11-75662077-1	chr11	75661494	75662661	+	1	NA	exon (NM_008659, exon 12 of 32)	exon (NM_008659, exon 12 of 32)	6062	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
Merged-chr11-44584241-1	chr11	44584135	44584348	+	1	NA	Intergenic	L1Md_T|LINE|L1	-2076	NR_126460	75389	Mm.261421	NR_126460	ENSMUSG00000086501	4930597A21Rik	-	RIKEN cDNA 4930597A21 gene	ncRNA
Merged-chr11-58679910-1	chr11	58679826	58679994	+	1	NA	Intergenic	L1Md_A|LINE|L1	-3965	NM_207230	216783	Mm.377240	NM_207230	ENSMUSG00000107711	Olfr320	GA_x6K02T2NKPP-730312-729392|MOR285-4|MOR285-5|Olfr321-ps1	olfactory receptor 320	protein-coding
Merged-chr10-27356352-1	chr10	27356230	27356474	+	1	NA	intron (NM_008481, intron 7 of 63)	L1Md_A|LINE|L1	-33514	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
Merged-chr19-27402223-1	chr19	27402121	27402325	+	1	NA	intron (NM_177474, intron 13 of 17)	L1Md_T|LINE|L1	27685	NR_131940	52874	Mm.261027	NM_177474	ENSMUSG00000041360	Pum3	1110069H02Rik|AA675048|D19Bwg1357e	pumilio RNA-binding family member 3	protein-coding
Merged-chr15-76195846-1	chr15	76195714	76195979	+	1	NA	promoter-TSS (NM_201394)	promoter-TSS (NM_201394)	-136	NM_201394	18810	Mm.234912	NM_011117	ENSMUSG00000022565	Plec	AA591047|AU042537|EBS1|PCN|PLTN|Plec1	plectin	protein-coding
Merged-chr1-143967253-1	chr1	143967133	143967374	+	1	NA	Intergenic	L1Md_A|LINE|L1	36896	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
Merged-chr12-32416675-1	chr12	32416576	32416775	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	37886	NM_001162903	72123	Mm.341352	NM_028111	ENSMUSG00000090946	Ccdc71l	2010109K11Rik|AV375874	coiled-coil domain containing 71 like	protein-coding
Merged-chr1-20490675-1	chr1	20490586	20490764	+	1	NA	intron (NM_153179, intron 35 of 66)	L1Md_A|LINE|L1	127382	NM_153179	241035	Mm.249253	NM_153179	ENSMUSG00000043760	Pkhd1	AI118496|AI182499|FPC|Tigm1	polycystic kidney and hepatic disease 1	protein-coding
Merged-chr13-66654548-1	chr13	66654460	66654637	+	1	NA	Intergenic	L1Md_T|LINE|L1	-213430	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr5-119726748-1	chr5	119726644	119726853	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-35530	NR_040416	433944	Mm.491053	NR_040416	ENSMUSG00000086847	Tbx3os2	Gm16065	T-box 3, opposite strand 2	ncRNA
Merged-chr1-56459220-1	chr1	56459094	56459346	+	1	NA	Intergenic	L1Md_T|LINE|L1	178231	NM_027661	71066	Mm.152656	NM_027661	ENSMUSG00000045336	Hsfy2	4933413G11Rik|Hspy2l	heat shock transcription factor, Y-linked 2	protein-coding
Merged-chr15-79962764-1	chr15	79962671	79962858	+	1	NA	Intergenic	Intergenic	-30118	NM_144811	52609	Mm.323442	NM_144811	ENSMUSG00000053411	Cbx7	1600014J01Rik|AI851678|D15Ertd417e	chromobox 7	protein-coding
Merged-chr13-68119285-1	chr13	68119194	68119376	+	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	112535	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr8-27310031-1	chr8	27309951	27310112	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	13986	NR_003107	732482	Mm.463248	NR_003107		Gm9731	-	Fam58a pseudogene	pseudo
Merged-chr15-87672120-1	chr15	87671967	87672274	+	1	NA	intron (NM_134096, intron 1 of 3)	intron (NM_134096, intron 1 of 3)	46890	NM_134096	106014	Mm.244319	NM_134096	ENSMUSG00000054863	Fam19a5	TAFA5|Tafa-5|Tara-5	family with sequence similarity 19, member A5	protein-coding
Merged-chr1-143862980-1	chr1	143862701	143863259	+	1	NA	Intergenic	L1Md_T|LINE|L1	85702	NM_019562	56207	Mm.261004	NM_019562	ENSMUSG00000018189	Uchl5	5830413B11Rik|Uch37	ubiquitin carboxyl-terminal esterase L5	protein-coding
Merged-chr12-66169606-1	chr12	66169495	66169717	+	1	NA	Intergenic	L1Md_A|LINE|L1	114795	NM_001162933	238217	Mm.188575	NM_001162933	ENSMUSG00000060499	Rpl10l	EG238217	ribosomal protein L10-like	protein-coding
Merged-chr13-100412607-1	chr13	100412427	100412788	+	1	NA	intron (NM_008670, intron 14 of 15)	intron (NM_008670, intron 14 of 15)	40257	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
Merged-chr11-56737863-1	chr11	56737746	56737981	+	1	NA	Intergenic	L1Md_T|LINE|L1	-273755	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
Merged-chr13-66648088-1	chr13	66647697	66648479	+	1	NA	Intergenic	L1_Mus3|LINE|L1	-206970	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-107330591-1	chr10	107330508	107330674	+	1	NA	intron (NM_001039354, intron 2 of 5)	L1Md_A|LINE|L1	58197	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
Merged-chr11-105706734-1	chr11	105706642	105706826	+	1	NA	intron (NM_181071, intron 3 of 25)	L1Md_T|LINE|L1	116748	NM_181071	77097	Mm.22501	NM_175492	ENSMUSG00000053580	Tanc2	3526402J09Rik|5730590C14Rik	tetratricopeptide repeat, ankyrin repeat and coiled-coil containing 2	protein-coding
Merged-chr15-102358228-1	chr15	102358146	102358310	+	1	NA	exon (NM_130458, exon 2 of 2)	exon (NM_130458, exon 2 of 2)	7401	NR_155425	102640093	Mm.385825	NR_155425	ENSMUSG00000116402	Gm36246	-	predicted gene, 36246	ncRNA
Merged-chr13-66795443-1	chr13	66795354	66795532	+	1	NA	Intergenic	MurSatRep1|Unknown|Unknown	109907	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr17-23359990-1	chr17	23359911	23360069	+	1	NA	exon (NM_001104579, exon 6 of 6)	exon (NM_001104579, exon 6 of 6)	16013	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr1-30307219-1	chr1	30307075	30307363	+	1	NA	Intergenic	L1Md_A|LINE|L1	556037	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik	PHD finger protein 3	protein-coding
Merged-chr17-21256300-1	chr17	21256209	21256392	+	1	NA	Intergenic	Intergenic	-4127	NM_134199	171233	Mm.222636	NM_134199	ENSMUSG00000050102	Vmn1r235	V1rf2	vomeronasal 1 receptor 235	protein-coding
Merged-chr6-121571735-1	chr6	121571623	121571847	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-64438	NM_175628	232345	Mm.30151	NM_175628	ENSMUSG00000030111	A2m	A2mp	alpha-2-macroglobulin	protein-coding
Merged-chr2-122265251-1	chr2	122265167	122265335	+	1	NA	TTS (NM_146126)	TTS (NM_146126)	30412	NM_146126	20322	Mm.371580	NM_146126	ENSMUSG00000027227	Sord	Sdh-1|Sdh1|Sodh-1	sorbitol dehydrogenase	protein-coding
Merged-chr13-100397889-1	chr13	100397795	100397984	+	1	NA	Intergenic	RLTR17|LTR|ERVK	54975	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
Merged-chr1-112930574-1	chr1	112930461	112930688	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-1065656	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr12-35905985-1	chr12	35905744	35906226	+	1	NA	Intergenic	L1Md_T|LINE|L1	-19636	NM_207531	403205	Mm.190508	NM_207531	ENSMUSG00000036231	Agr3	BCMP11|E030025L21Rik|Gm888	anterior gradient 3	protein-coding
Merged-chr13-66666776-1	chr13	66666613	66666939	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-225658	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-103316335-1	chr15	103316175	103316495	+	1	NA	intron (NM_001356627, intron 4 of 7)	intron (NM_001356627, intron 4 of 7)	-5897	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
Merged-chr15-101485639-1	chr15	101485518	101485761	+	1	NA	intron (NM_001201323, intron 8 of 8)	intron (NM_001201323, intron 8 of 8)	5664	NM_016879	53622	Mm.347934	NM_016879		Krt85	AA589597|BB007925|Hb5|Krt2-18	keratin 85	protein-coding
Merged-chr19-5932910-1	chr19	5932826	5932995	+	1	NA	Intergenic	CT-rich|Low_complexity|Low_complexity	-8094	NM_026772	104252	Mm.491103	NM_026772	ENSMUSG00000045664	Cdc42ep2	1110008C05Rik|Borg1|Cep2|D19Bwg1013e	CDC42 effector protein (Rho GTPase binding) 2	protein-coding
Merged-chr1-169109917-1	chr1	169109790	169110045	+	1	NA	Intergenic	L1Md_A|LINE|L1	-90828	NR_105772	102466632		NR_105772	ENSMUSG00000098829	Mir6354	Gm27282|mmu-mir-6354	microRNA 6354	ncRNA
Merged-chr13-100422157-1	chr13	100422043	100422271	+	1	NA	intron (NM_008670, intron 12 of 15)	RMER21B|LTR|ERV1	30707	NM_008670	17940	Mm.6898	NM_008670	ENSMUSG00000021640	Naip1	AV364616|Birc1a|D13Lsd1|Naip|Naip-rs1	NLR family, apoptosis inhibitory protein 1	protein-coding
Merged-chr10-46582699-1	chr10	46582601	46582797	+	1	NA	Intergenic	L1Md_A|LINE|L1	337950	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr19-4117189-1	chr19	4117073	4117305	+	1	NA	intron (NM_016666, intron 3 of 6)	B3A|SINE|B2	4386	NM_001276284	11632	Mm.10433	NM_016666	ENSMUSG00000024847	Aip	AA408703|AW476050|Ara9|D19Bwg1412e|Fkbp16|Xap2	aryl-hydrocarbon receptor-interacting protein	protein-coding
Merged-chr8-19954559-1	chr8	19954477	19954641	+	1	NA	intron (NM_001270553, intron 6 of 9)	RLTR13D5|LTR|ERVK	224983	NM_001270553	100861668	Mm.491087	NM_001270553	ENSMUSG00000095294	Gm21119	-	predicted gene, 21119	protein-coding
Merged-chr13-66676530-1	chr13	66676436	66676625	+	1	NA	Intergenic	MTE-int|LTR|ERVL-MaLR	228820	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr10-87634184-1	chr10	87634087	87634281	+	1	NA	Intergenic	L1Md_T|LINE|L1	112389	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
Merged-chr13-66630996-1	chr13	66630724	66631269	+	1	NA	Intergenic	RLTR45-int|LTR|ERVK	-189878	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr12-68435411-1	chr12	68435324	68435498	+	1	NA	Intergenic	L1Md_T|LINE|L1	723775	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr5-88162748-1	chr5	88162639	88162858	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	76192	NM_001252681	20600	Mm.1397	NM_021289	ENSMUSG00000029281	Smr2	MSG2|Vcs2	submaxillary gland androgen regulated protein 2	protein-coding
Merged-chr19-46397367-1	chr19	46397288	46397446	+	1	NA	intron (NM_001025391, intron 1 of 11)	intron (NM_001025391, intron 1 of 11)	471	NM_001025391	24069	Mm.41210	NM_015752	ENSMUSG00000025231	Sufu	Su(fu)	SUFU negative regulator of hedgehog signaling	protein-coding
Merged-chr3-124160718-1	chr3	124160601	124160835	+	1	NA	Intergenic	L1Md_A|LINE|L1	-160319	NM_146140	229801	Mm.165810	NM_146140	ENSMUSG00000044528	Tram1l1	A830091N21Rik	translocation associated membrane protein 1-like 1	protein-coding
Merged-chr5-113771656-1	chr5	113771548	113771765	+	1	NA	non-coding (NR_151532, exon 1 of 17)	non-coding (NR_151532, exon 1 of 17)	744	NR_151532	53890	Mm.29594	NM_016926	ENSMUSG00000018974	Sart3	AU045857|mKIAA0156	squamous cell carcinoma antigen recognized by T cells 3	protein-coding
Merged-chr1-50333735-1	chr1	50333527	50333944	+	1	NA	Intergenic	L1Md_T|LINE|L1	-593788	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
Merged-chr10-87632119-1	chr10	87631984	87632254	+	1	NA	Intergenic	L1Md_T|LINE|L1	110324	NM_008777	18478	Mm.263539	NM_008777	ENSMUSG00000020051	Pah	AW106920	phenylalanine hydroxylase	protein-coding
Merged-chr11-81139247-1	chr11	81139132	81139363	+	1	NA	intron (NM_001034013, intron 1 of 9)	L1Md_T|LINE|L1	13656	NM_007384	11418	Mm.234998	NM_007384	ENSMUSG00000020704	Asic2	ACIC2|Accn1|BNC1|BNaC1|BNaC1a|Mdeg	acid-sensing (proton-gated) ion channel 2	protein-coding
Merged-chr11-38014142-1	chr11	38014057	38014228	+	1	NA	Intergenic	L1Md_T|LINE|L1	355153	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr16-22278786-1	chr16	22278686	22278886	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-12781	NM_009186	20462	Mm.210352	NM_009186	ENSMUSG00000022858	Tra2b	5730405G21Rik|D16Ertd266e|SIG-41|Sfrs10|Silg41|TRA2beta	transformer 2 beta	protein-coding
Merged-chr17-17225713-1	chr17	17225627	17225799	+	1	NA	Intergenic	RMER3D-int|LTR|ERVK	-9190	NM_001362181	102640673		NM_001362181		LOC102640673	-	zinc finger protein 431-like	protein-coding
Merged-chr19-7314344-1	chr19	7314253	7314435	+	1	NA	intron (NM_001080388, intron 1 of 16)	G-rich|Low_complexity|Low_complexity	-18897	NM_001080390	13728	Mm.258986	NM_007928	ENSMUSG00000024969	Mark2	EMK-1|Emk|Par-1|Par-1b	MAP/microtubule affinity regulating kinase 2	protein-coding
Merged-chr1-114105047-1	chr1	114104943	114105151	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1580090	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr1-186105477-1	chr1	186105321	186105634	+	1	NA	intron (NM_146106, intron 2 of 4)	L1Md_T|LINE|L1	11833	NM_146106	226791	Mm.257116	NM_146106	ENSMUSG00000039246	Lyplal1	BC027340|Q96AVO	lysophospholipase-like 1	protein-coding
Merged-chr12-13422455-1	chr12	13422331	13422579	+	1	NA	intron (NM_027706, intron 35 of 51)	L1Md_T|LINE|L1	153328	NM_027706	71169	Mm.177520	NM_027706	ENSMUSG00000020576	Nbas	4933425L03Rik|Nag	neuroblastoma amplified sequence	protein-coding
Merged-chr11-93805451-1	chr11	93805360	93805543	+	1	NA	Intergenic	L1Md_T|LINE|L1	80315	NM_001013375	217109	Mm.379350	NM_001013375	ENSMUSG00000054079	Utp18	6230425C22Rik|6430513M13|Wdr50	UTP18 small subunit processome component	protein-coding
Merged-chr5-146493148-1	chr5	146492957	146493339	+	1	NA	exon (NM_001243110, exon 4 of 5)	exon (NM_001243110, exon 4 of 5)	1785	NM_001243110	622924	Mm.389722	NM_001243110	ENSMUSG00000096527	Gm6370	-	predicted gene 6370	protein-coding
Merged-chr11-64302567-1	chr11	64302461	64302673	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132765	NM_178870	15478	Mm.340214	NM_178870	ENSMUSG00000047759	Hs3st3a1	3Ost3a|Hs3st3a	heparan sulfate (glucosamine) 3-O-sulfotransferase 3A1	protein-coding
Merged-chr10-113388023-1	chr10	113387924	113388123	+	1	NA	Intergenic	L1Md_A|LINE|L1	-458997	NM_001033474	382423	Mm.431239	NM_001033474	ENSMUSG00000074748	Atxn7l3b	4921506J03Rik|6230409E21Rik|AI315132	ataxin 7-like 3B	protein-coding
Merged-chr1-176541700-1	chr1	176541551	176541849	+	1	NA	Intergenic	L1Md_T|LINE|L1	-14431	NR_151528	102640488	Mm.415515	NR_151528	ENSMUSG00000104021	Gm36536	-	predicted gene, 36536	ncRNA
Merged-chr8-71507047-1	chr8	71506922	71507173	+	1	NA	exon (NM_032398, exon 4 of 6)	exon (NM_032398, exon 4 of 6)	4722	NM_032398	84094	Mm.260768	NM_032398	ENSMUSG00000034845	Plvap	MECA32|Pv1	plasmalemma vesicle associated protein	protein-coding
Merged-chr1-79383812-1	chr1	79383482	79384142	+	1	NA	Intergenic	L1Md_T|LINE|L1	56278	NM_001310680	20254	Mm.5038	NM_009129	ENSMUSG00000050711	Scg2	Chgc|SgII	secretogranin II	protein-coding
Merged-chr12-27241847-1	chr12	27241759	27241936	+	1	NA	Intergenic	L1Md_A|LINE|L1	-81331	NR_045869	636791	Mm.423496	NM_001039248	ENSMUSG00000094002	Gm9866	EG636791	predicted gene 9866	ncRNA
Merged-chr15-54841975-1	chr15	54841896	54842055	+	1	NA	intron (NM_001285994, intron 25 of 25)	intron (NM_001285994, intron 25 of 25)	78171	NM_015744	18606	Mm.250256	NM_015744	ENSMUSG00000022425	Enpp2	ATX|E-NPP 2|Npps2|PD-Ialpha|Pdnp2|lysoPLD	ectonucleotide pyrophosphatase/phosphodiesterase 2	protein-coding
Merged-chr1-82550709-1	chr1	82550482	82550936	+	1	NA	intron (NM_007735, intron 4 of 47)	L1Md_A|LINE|L1	36140	NM_007735	12829	Mm.40253	NM_007735	ENSMUSG00000067158	Col4a4	E130010M05Rik|[a]4(IV)	collagen, type IV, alpha 4	protein-coding
Merged-chr1-166913365-1	chr1	166913190	166913541	+	1	NA	Intergenic	L1Md_T|LINE|L1	86365	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
Merged-chr16-69002662-1	chr16	69002578	69002746	+	1	NA	Intergenic	L1Md_T|LINE|L1	797719	NR_130991	78110	Mm.211406	NR_130991	ENSMUSG00000107073	4930428D20Rik	Gm43265	RIKEN cDNA 4930428D20 gene	ncRNA
Merged-chr1-73321244-1	chr1	73321160	73321328	+	1	NA	Intergenic	L1Md_T|LINE|L1	-77724	NR_040605	78718	Mm.244075	NR_040605	ENSMUSG00000101812	D530049I02Rik	-	RIKEN cDNA D530049I02 gene	ncRNA
Merged-chr11-22771676-1	chr11	22771523	22771830	+	1	NA	Intergenic	L1Md_F2|LINE|L1	88059	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
Merged-chr1-158335030-1	chr1	158334935	158335126	+	1	NA	intron (NM_207583, intron 1 of 7)	L1Md_T|LINE|L1	21230	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
Merged-chr15-42400954-1	chr15	42400843	42401065	+	1	NA	Intergenic	L1Md_F2|LINE|L1	276023	NM_009640	11600	Mm.309336	NM_009640	ENSMUSG00000022309	Angpt1	1110046O21Rik|Ang-1|Ang1	angiopoietin 1	protein-coding
Merged-chr12-60467134-1	chr12	60467042	60467226	+	1	NA	Intergenic	L1Md_A|LINE|L1	1054686	NR_045049	100504101	Mm.235026	NR_045049	ENSMUSG00000113429	Gm20063	-	predicted gene, 20063	ncRNA
Merged-chr17-35320608-1	chr17	35320511	35320706	+	1	NA	promoter-TSS (NM_001358790)	promoter-TSS (NM_001358790)	61	NM_001358790	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
Merged-chr15-89324168-1	chr15	89324059	89324278	+	1	NA	exon (NM_182928, exon 3 of 3)	exon (NM_182928, exon 3 of 3)	1448	NM_182928	223780	Mm.210541	NM_182928	ENSMUSG00000054136	Adm2	Am2|IMD|Imdn	adrenomedullin 2	protein-coding
Merged-chr13-42175880-1	chr13	42175789	42175971	+	1	NA	intron (NM_007772, intron 7 of 8)	MTA_Mm|LTR|ERVL-MaLR	123859	NM_007772	110521	Mm.4808	NM_007772	ENSMUSG00000021366	Hivep1	Cryabp1	human immunodeficiency virus type I enhancer binding protein 1	protein-coding
Merged-chr13-65350859-1	chr13	65350706	65351013	+	1	NA	Intergenic	RLTR33|LTR|ERVK	72005	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
Merged-chr8-113602012-1	chr8	113601892	113602132	+	1	NA	Intergenic	L1Md_A|LINE|L1	-33574	NM_001048143	270096	Mm.74689	NM_173015	ENSMUSG00000078908	Mon1b	5031407H10|5033413H12Rik	MON1 homolog B, secretory traffciking associated	protein-coding
Merged-chr19-31995706-1	chr19	31995619	31995794	+	1	NA	intron (NM_018830, intron 21 of 23)	MTA_Mm|LTR|ERVL-MaLR	107434	NM_018830	54447	Mm.491229	NM_018830	ENSMUSG00000024887	Asah2	AI585898	N-acylsphingosine amidohydrolase 2	protein-coding
Merged-chr15-79169577-1	chr15	79169461	79169694	+	1	NA	intron (NR_029470, intron 1 of 4)	intron (NR_029470, intron 1 of 4)	3511	NR_029470	100041655	Mm.483310	NR_029470	ENSMUSG00000075555	Gm10863	-	predicted gene 10863	ncRNA
Merged-chr19-37351605-1	chr19	37351518	37351692	+	1	NA	Intergenic	PB1D10|SINE|Alu	-20992	NM_031156	15925	Mm.28366	NM_031156	ENSMUSG00000056999	Ide	1300012G03Rik|4833415K22Rik|AA675336|AI507533	insulin degrading enzyme	protein-coding
Merged-chr10-35355566-1	chr10	35355472	35355661	+	1	NA	Intergenic	L1Md_A|LINE|L1	872166	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
Merged-chr17-23346255-1	chr17	23346174	23346336	+	1	NA	exon (NM_001104579, exon 3 of 6)	exon (NM_001104579, exon 3 of 6)	2278	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr10-43261471-1	chr10	43261221	43261722	+	1	NA	intron (NM_027772, intron 1 of 7)	L1Md_A|LINE|L1	39985	NM_027772	71365	Mm.490430	NM_027772	ENSMUSG00000038240	Pdss2	5430420P03Rik|Gm60|Plmp|kd|mDLP1	prenyl (solanesyl) diphosphate synthase, subunit 2	protein-coding
Merged-chr4-96054444-1	chr4	96054351	96054538	+	1	NA	intron (NM_001346540, intron 6 of 6)	IAPEz-int|LTR|ERVK	23096	NM_145548	230459	Mm.268175	NM_145548	ENSMUSG00000028571	Cyp2j13	-	cytochrome P450, family 2, subfamily j, polypeptide 13	protein-coding
Merged-chr13-66435817-1	chr13	66435735	66435899	+	1	NA	intron (NM_001290196, intron 1 of 3)	Lx4B|LINE|L1	5301	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-7333864-1	chr1	7333765	7333963	+	1	NA	Intergenic	L1Md_T|LINE|L1	244944	NM_183028	319263	Mm.21539	NM_183028	ENSMUSG00000051285	Pcmtd1	8430411F12Rik|A030012M09Rik	protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 1	protein-coding
Merged-chr15-62602733-1	chr15	62602626	62602841	+	1	NA	Intergenic	Lx4A|LINE|L1	-383282	NR_003523	67552	Mm.484027	NM_026230		H2afy3	4933432H23Rik	H2A histone family, member Y3	pseudo
Merged-chr13-68443446-1	chr13	68443314	68443578	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-86621	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr12-115185665-1	chr12	115185507	115185824	+	1	NA	Intergenic	Intergenic	510129	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-115889404-1	chr1	115889313	115889496	+	1	NA	intron (NM_001077425, intron 1 of 23)	IAPEz-int|LTR|ERVK	204267	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr1-101758928-1	chr1	101758843	101759014	+	1	NA	Intergenic	L1Md_T|LINE|L1	603160	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr1-173256853-1	chr1	173256723	173256984	+	1	NA	Intergenic	L1Md_A|LINE|L1	-13294	NM_146651	258645	Mm.377611	NM_146651	ENSMUSG00000049605	Olfr418	MOR267-12P|MOR267-8|Olfr1403|Olfr418-ps1	olfactory receptor 418	protein-coding
Merged-chr10-31609660-1	chr10	31609574	31609747	+	1	NA	promoter-TSS (NM_001146349)	promoter-TSS (NM_001146349)	65	NM_001146349	268291	Mm.295212	NM_001146349	ENSMUSG00000063760	Rnf217	AU016819|Ibrdc1	ring finger protein 217	protein-coding
Merged-chr15-86055972-1	chr15	86055848	86056097	+	1	NA	Intergenic	MLT1B|LTR|ERVL-MaLR	-1723	NM_172611	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
Merged-chr13-66642428-1	chr13	66642169	66642688	+	1	NA	Intergenic	Intergenic	-201310	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr11-18624439-1	chr11	18624355	18624524	+	1	NA	Intergenic	L1Md_A|LINE|L1	394530	NM_010789	17268	Mm.356578	NM_010789	ENSMUSG00000020160	Meis1	C530044H18Rik|Evi8	Meis homeobox 1	protein-coding
Merged-chr10-57770463-1	chr10	57770351	57770576	+	1	NA	Intergenic	L1Md_T|LINE|L1	-14460	NM_021272	12140	Mm.3644	NM_021272	ENSMUSG00000019874	Fabp7	B-FABP|BFABP|Blbp|MRG	fatty acid binding protein 7, brain	protein-coding
Merged-chr11-44462767-1	chr11	44462641	44462893	+	1	NA	intron (NM_024475, intron 6 of 10)	GA-rich|Low_complexity|Low_complexity	7781	NM_024475	79560	Mm.338784	NM_024475	ENSMUSG00000041231	Ublcp1	4930527B16Rik|8430435I17Rik|BC002236	ubiquitin-like domain containing CTD phosphatase 1	protein-coding
Merged-chr11-96100171-1	chr11	96100072	96100270	+	1	NA	exon (NM_001271018, exon 6 of 6)	exon (NM_001271018, exon 6 of 6)	11791	NM_001271018	76815	Mm.296049	NM_029755	ENSMUSG00000006056	Calcoco2	2410154J16Rik|C77254|Ndp52|Ndp52l1	calcium binding and coiled-coil domain 2	protein-coding
Merged-chr4-98648784-1	chr4	98648680	98648888	+	1	NA	intron (NM_001005787, intron 6 of 15)	L1Md_T|LINE|L1	51971	NR_151609	102638531		NR_151609		Gm35073	-	predicted gene, 35073	ncRNA
Merged-chr6-145338002-1	chr6	145337854	145338150	+	1	NA	Intergenic	Intergenic	-49623	NR_003625	381827	Mm.179075	NM_001001987		1700073E17Rik	-	ribosomal protein L7 pseudogene	pseudo
Merged-chrX-3268039-1	chrX	3267922	3268156	+	1	NA	Intergenic	L1Md_F2|LINE|L1	175651	NM_001085552	668960		NM_001085552	ENSMUSG00000095716	Btbd35f10	Gm14351	BTB domain containing 35, family member 10	protein-coding
Merged-chr8-74586845-1	chr8	74586730	74586961	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-286329	NM_027837	71597	Mm.158735	NM_027837	ENSMUSG00000031621	Isx	9130012O13Rik|Pix-1	intestine specific homeobox	protein-coding
Merged-chr10-80142659-1	chr10	80142576	80142743	+	1	NA	intron (NM_001347092, intron 1 of 2)	intron (NM_001347092, intron 1 of 2)	344	NM_025313	66043	Mm.278560	NM_025313	ENSMUSG00000003072	Atp5d	0610008F14Rik|1500000I11Rik|AA960090|AI876556|AU020773|Atp5f1d|C85518	ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit	protein-coding
Merged-chr11-8155725-1	chr11	8155641	8155810	+	1	NA	Intergenic	L1Md_T|LINE|L1	508810	NM_001083587	319939	Mm.337820	NM_001083587	ENSMUSG00000020422	Tns3	BC023928|F830010I22Rik|TEM6|Tens1	tensin 3	protein-coding
Merged-chr10-79944781-1	chr10	79944683	79944880	+	1	NA	intron (NM_001288625, intron 3 of 8)	intron (NM_001288625, intron 3 of 8)	-15371	NM_175450	216156	Mm.35828	NM_175450	ENSMUSG00000035754	Wdr18	2310012I10Rik|AU044733|AW122032	WD repeat domain 18	protein-coding
Merged-chr6-122887742-1	chr6	122887630	122887854	+	1	NA	3' UTR (NM_026267, exon 8 of 8)	3' UTR (NM_026267, exon 8 of 8)	13185	NM_026267	67602	Mm.288114	NM_026267	ENSMUSG00000030327	Necap1	1200016B17Rik|AI747569|mFLJ00061	NECAP endocytosis associated 1	protein-coding
Merged-chr15-4419795-1	chr15	4419650	4419940	+	1	NA	intron (NM_177355, intron 1 of 2)	L1Md_T|LINE|L1	44304	NM_177355	239318	Mm.308996	NM_177355	ENSMUSG00000049148	Plcxd3	B130016O10Rik	phosphatidylinositol-specific phospholipase C, X domain containing 3	protein-coding
Merged-chr13-118527842-1	chr13	118527717	118527967	+	1	NA	Intergenic	L1Md_A|LINE|L1	-28326	NR_045982	75890	Mm.141235	NR_045982	ENSMUSG00000100727	1700003P14Rik	1700030O10Rik|4930584L06Rik	RIKEN cDNA 1700003P14 gene	ncRNA
Merged-chr1-42143023-1	chr1	42142817	42143230	+	1	NA	Intergenic	L1Md_A|LINE|L1	551802	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
Merged-chr1-80136784-1	chr1	80136669	80136900	+	1	NA	Intergenic	L1Md_T|LINE|L1	77160	NM_173425	241128	Mm.145511	NM_173425	ENSMUSG00000043230	Fam124b	A830043J08Rik	family with sequence similarity 124, member B	protein-coding
Merged-chr10-59030080-1	chr10	59029965	59030195	+	1	NA	intron (NM_172788, intron 3 of 9)	L1Md_A|LINE|L1	191767	NM_001024911	103080	Mm.346842	NM_001024910	ENSMUSG00000019917	Sept10	4921515A04Rik|9430099J10Rik|AA408298|AI874685	septin 10	protein-coding
Merged-chr8-72889743-1	chr8	72889655	72889832	+	1	NA	intron (NM_001317391, intron 8 of 15)	L1Md_A|LINE|L1	-126769	NR_039551	100628574		NR_039551	ENSMUSG00000093140	Mir28b	mmu-mir-28b	microRNA 28b	ncRNA
Merged-chr15-77442825-1	chr15	77442735	77442916	+	1	NA	intron (NM_001024848, intron 1 of 4)	intron (NM_001024848, intron 1 of 4)	4635	NM_001024848	278679	Mm.440965	NM_001024848	ENSMUSG00000068252	Apol7b	-	apolipoprotein L 7b	protein-coding
Merged-chr1-63833314-1	chr1	63833195	63833434	+	1	NA	Intergenic	L1Md_A|LINE|L1	-64047	NM_001256158	74426	Mm.159197	NM_001256158	ENSMUSG00000025961	4933402D24Rik	-	RIKEN cDNA 4933402D24 gene	protein-coding
Merged-chr11-26431753-1	chr11	26431644	26431863	+	1	NA	intron (NM_001277273, intron 6 of 13)	L1Md_T|LINE|L1	44669	NR_102382	67030	Mm.18875	NM_025923	ENSMUSG00000004018	Fancl	2010322C19Rik|AW554273|B230118H11Rik|Phf9|Pog|gcd	Fanconi anemia, complementation group L	protein-coding
Merged-chr15-52465067-1	chr15	52464984	52465150	+	1	NA	Intergenic	L2a|LINE|L2	169514	NM_172816	239436	Mm.208831	NM_172816	ENSMUSG00000022315	Slc30a8	C820002P14Rik|ZnT-8|ZnT8	solute carrier family 30 (zinc transporter), member 8	protein-coding
Merged-chr8-70863536-1	chr8	70863447	70863625	+	1	NA	Intergenic	Intergenic	-6528	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
Merged-chr15-89279145-1	chr15	89279064	89279226	+	1	NA	intron (NM_026813, intron 16 of 24)	intron (NM_026813, intron 16 of 24)	26587	NR_105924	102465981		NR_105924	ENSMUSG00000098442	Mir6959	Gm27807|mmu-mir-6959	microRNA 6959	ncRNA
Merged-chr16-28500731-1	chr16	28500634	28500829	+	1	NA	intron (NM_010199, intron 2 of 5)	L1Md_A|LINE|L1	-54656	NM_001276420	14167	Mm.7996	NM_010199	ENSMUSG00000022523	Fgf12	AV114868|B230343J05Rik|FGF-12|FHF-1|Fhf1	fibroblast growth factor 12	protein-coding
Merged-chr16-94482094-1	chr16	94482012	94482177	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	44535	NM_007834	13185	Mm.7472	NM_007834	ENSMUSG00000022898	Dscr3	AW538125|Dcra	DSCR3 arrestin fold containing	protein-coding
Merged-chr1-117169993-1	chr1	117169860	117170126	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	1140735	NR_153836	22099	Mm.426637	NM_011650	ENSMUSG00000026374	Tsn	2610034C24Rik|AU040286|C3PO|TB-RBP	translin	protein-coding
Merged-chr15-40715081-1	chr15	40714988	40715174	+	1	NA	intron (NM_001356998, intron 1 of 6)	intron (NM_001356998, intron 1 of 6)	60039	NM_001356998	22762	Mm.39496	NM_011766	ENSMUSG00000022306	Zfpm2	B330005D23Rik|FOG-2|FOG2	zinc finger protein, multitype 2	protein-coding
Merged-chr19-38112644-1	chr19	38112552	38112736	+	1	NA	intron (NM_181748, intron 2 of 2)	intron (NM_181748, intron 2 of 2)	12167	NM_011255	19662	Mm.2605	NM_011255	ENSMUSG00000024990	Rbp4	Rbp-4	retinol binding protein 4, plasma	protein-coding
Merged-chr10-80820106-1	chr10	80820004	80820208	+	1	NA	Intergenic	ZP3AR|Satellite|Satellite	-6550	NM_008753	18245	Mm.398119	NM_008753	ENSMUSG00000035242	Oaz1	AZ-1|AZ1|Antizyme|ODC-Az|Oaz	ornithine decarboxylase antizyme 1	protein-coding
Merged-chrX-82660968-1	chrX	82660846	82661090	+	1	NA	Intergenic	L1Md_T|LINE|L1	-287902	NM_007868	13405	Mm.275608	NM_007868	ENSMUSG00000045103	Dmd	DXSmh7|DXSmh9|Dp427|Dp71|dys|mdx|pke	dystrophin, muscular dystrophy	protein-coding
Merged-chr8-84860906-1	chr8	84860824	84860989	+	1	NA	exon (NM_025648, exon 2 of 13)	exon (NM_025648, exon 2 of 13)	3920	NM_025648	66590	Mm.292517	NM_025648	ENSMUSG00000003808	Farsa	0610012A19Rik|Farsla|pheRS	phenylalanyl-tRNA synthetase, alpha subunit	protein-coding
Merged-chr1-114735252-1	chr1	114735112	114735392	+	1	NA	Intergenic	L1Md_A|LINE|L1	-949885	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr11-99685367-1	chr11	99685233	99685502	+	1	NA	Intergenic	Intergenic	-19407	NM_026834	68768	Mm.416844	NM_026834	ENSMUSG00000075566	Krtap4-6	1110054P19Rik	keratin associated protein 4-6	protein-coding
Merged-chr10-33827568-1	chr10	33827426	33827710	+	1	NA	Intergenic	L1Md_T|LINE|L1	-30154	NM_020565	57430	Mm.6590	NM_020565	ENSMUSG00000069668	Sult3a1	ST3A1|Sult-x2|Sultx2	sulfotransferase family 3A, member 1	protein-coding
Merged-chr15-76258095-1	chr15	76258013	76258178	+	1	NA	Intergenic	Intergenic	9904	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
Merged-chr15-86073733-1	chr15	86073612	86073855	+	1	NA	intron (NM_001205353, intron 1 of 18)	intron (NM_001205353, intron 1 of 18)	15006	NM_001205353	223752	Mm.24442	NM_172611	ENSMUSG00000035900	Gramd4	9930016O13	GRAM domain containing 4	protein-coding
Merged-chr1-76464422-1	chr1	76464303	76464542	+	1	NA	Intergenic	L1Md_T|LINE|L1	-24711	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA
Merged-chr13-74357804-1	chr13	74357690	74357918	+	1	NA	3' UTR (NM_001168659, exon 3 of 3)	3' UTR (NM_001168659, exon 3 of 3)	6196	NM_001033042	432779	Mm.324679	NM_001033042	ENSMUSG00000021579	Lrrc14b	AI595366	leucine rich repeat containing 14B	protein-coding
Merged-chr1-155756675-1	chr1	155756536	155756814	+	1	NA	Intergenic	L1Md_A|LINE|L1	-14648	NM_010712	16872	Mm.103624	NM_010712	ENSMUSG00000026468	Lhx4	A330062J17Rik|Gsh-4|Gsh4	LIM homeobox protein 4	protein-coding
Merged-chr1-46447816-1	chr1	46447728	46447905	+	1	NA	intron (NM_001310335, intron 3 of 64)	L1Md_T|LINE|L1	22298	NM_001310335	100101919	Mm.383402	NM_001310335	ENSMUSG00000101337	Dnah7c	Dnahc7c	dynein, axonemal, heavy chain 7C	protein-coding
Merged-chr1-176895174-1	chr1	176895080	176895269	+	1	NA	intron (NM_001357390, intron 13 of 18)	L1Md_A|LINE|L1	-59041	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
Merged-chr8-22706498-1	chr8	22706413	22706584	+	1	NA	promoter-TSS (NM_010546)	promoter-TSS (NM_010546)	85	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
Merged-chr7-107854957-1	chr7	107854776	107855138	+	1	NA	Intergenic	L1Md_T|LINE|L1	-9226	NM_146425	258417	Mm.377488	NM_146425	ENSMUSG00000109542	Olfr470	MOR204-22	olfactory receptor 470	protein-coding
Merged-chr1-165970731-1	chr1	165970600	165970863	+	1	NA	intron (NM_198932, intron 1 of 15)	L1Md_T|LINE|L1	31903	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
Merged-chr1-120997855-1	chr1	120997710	120998000	+	1	NA	Intergenic	L1Md_T|LINE|L1	-89550	NR_038008	98452	Mm.131017	NR_038008	ENSMUSG00000097881	Celrr	AI848258|B230209K01Rik|Celr|Gm818	cerebellum expressed regulatory RNA	ncRNA
Merged-chr19-3575778-1	chr19	3575694	3575862	+	1	NA	promoter-TSS (NM_028999)	promoter-TSS (NM_028999)	-29	NM_001360430	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
Merged-chr10-104893940-1	chr10	104893848	104894032	+	1	NA	Intergenic	L1Md_T|LINE|L1	606671	NR_105838	102465222		NR_105838	ENSMUSG00000099264	Mir6411	Gm27767|mmu-mir-6411	microRNA 6411	ncRNA
Merged-chr15-80186561-1	chr15	80186477	80186645	+	1	NA	intron (NM_010795, intron 1 of 1)	intron (NM_010795, intron 1 of 1)	12840	NM_010795	17309	Mm.299693	NM_010795	ENSMUSG00000042428	Mgat3	1110038J12Rik|AI848272|GnT-III	mannoside acetylglucosaminyltransferase 3	protein-coding
Merged-chr12-57602595-1	chr12	57602392	57602798	+	1	NA	intron (NR_131110, intron 2 of 4)	L1Md_T|LINE|L1	16007	NR_131110	78758	Mm.160125	NR_131110	ENSMUSG00000085851	4921518K17Rik	-	RIKEN cDNA 4921518K17 gene	ncRNA
Merged-chr15-7279430-1	chr15	7279311	7279550	+	1	NA	intron (NM_001289496, intron 6 of 22)	L1Md_T|LINE|L1	118960	NM_001289496	268780	Mm.203208	NM_178748	ENSMUSG00000042961	Egflam	5930412K08|AU040377	EGF-like, fibronectin type III and laminin G domains	protein-coding
Merged-chr15-36772152-1	chr15	36772054	36772250	+	1	NA	3' UTR (NM_011740, exon 7 of 7)	3' UTR (NM_011740, exon 7 of 7)	18780	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
Merged-chr7-44250924-1	chr7	44250787	44251062	+	1	NA	TTS (NR_028534)	TTS (NR_028534)	774	NR_028533	100217433		NR_028533	ENSMUSG00000095472	Snord88a	MBII-211	small nucleolar RNA, C/D box 88A	snoRNA
Merged-chr17-36136854-1	chr17	36136775	36136934	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	-7429	NM_001177467	630294	Mm.484916	NM_001177467	ENSMUSG00000092243	Gm7030	EG630294|H2-t9	predicted gene 7030	protein-coding
Merged-chr10-22327583-1	chr10	22327441	22327726	+	1	NA	intron (NM_009018, intron 6 of 6)	L1Md_F|LINE|L1	20863	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
Merged-chr6-125844423-1	chr6	125844336	125844510	+	1	NA	intron (NM_153589, intron 10 of 25)	MTA_Mm-int|LTR|ERVL-MaLR	154004	NM_153589	243634	Mm.333398	NM_153589	ENSMUSG00000038115	Ano2	BC033409|Tmem16b	anoctamin 2	protein-coding
Merged-chr1-48497738-1	chr1	48497617	48497859	+	1	NA	Intergenic	L1Md_A|LINE|L1	-746878	NR_151585	442837	Mm.337149	NM_001002792	ENSMUSG00000051616	C230029F24Rik	-	RIKEN cDNA C230029F24 gene	ncRNA
Merged-chr1-27165054-1	chr1	27164943	27165166	+	1	NA	Intergenic	L1Md_T|LINE|L1	-477594	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
Merged-chr10-90217660-1	chr10	90217577	90217743	+	1	NA	intron (NM_001359241, intron 9 of 25)	L1Md_T|LINE|L1	344151	NM_001128086	77531	Mm.440605	NM_181398	ENSMUSG00000058589	Anks1b	AIDA-1|AIDA-1b|C030032C09Rik|E530015N03Rik|EB-1|Gm10937|Gm1555	ankyrin repeat and sterile alpha motif domain containing 1B	protein-coding
Merged-chr17-53010132-1	chr17	53010028	53010236	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	407423	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
Merged-chr17-33161464-1	chr17	33161374	33161554	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-12715	NM_001360203	240069	Mm.157765	NM_177719	ENSMUSG00000048602	Morc2b	4932411A10Rik|Tce6	microrchidia 2B	protein-coding
Merged-chr15-75841714-1	chr15	75841593	75841836	+	1	NA	intron (NM_172121, intron 1 of 11)	CpG	194	NM_172121	223642	Mm.209800	NM_172121	ENSMUSG00000075600	Zc3h3	BC049953|Kiaa0150|Smicl|Zc3hdc3	zinc finger CCCH type containing 3	protein-coding
Merged-chr11-75665723-1	chr11	75665536	75665911	+	1	NA	exon (NM_008659, exon 16 of 32)	exon (NM_008659, exon 16 of 32)	9708	NM_001080775	17913	Mm.234502	NM_008659	ENSMUSG00000017774	Myo1c	C80397|MMIb|MYO1E|NMI|mm1beta|myr2	myosin IC	protein-coding
Merged-chr12-115616332-1	chr12	115616236	115616428	+	1	NA	Intergenic	Intergenic	79462	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr13-66476770-1	chr13	66476635	66476905	+	1	NA	Intergenic	B3A|SINE|B2	-35652	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-113896217-1	chr1	113896090	113896345	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1788920	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr12-10627447-1	chr12	10627358	10627536	+	1	NA	Intergenic	L1Md_A|LINE|L1	181059	NR_110487	328061	Mm.56067	NR_110487	ENSMUSG00000112792	Gm38407	4931412M21	predicted gene, 38407	ncRNA
Merged-chr13-66465190-1	chr13	66465088	66465293	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-24072	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-121939291-1	chr10	121939181	121939401	+	1	NA	intron (NM_001081037, intron 1 of 21)	L1Md_T|LINE|L1	108024	NM_001081037	117600	Mm.288698	NM_001081037	ENSMUSG00000020121	Srgap1	4930572H05Rik|Arhgap13	SLIT-ROBO Rho GTPase activating protein 1	protein-coding
Merged-chr1-128848033-1	chr1	128847867	128848200	+	1	NA	Intergenic	L1Md_A|LINE|L1	-255734	NM_009911	12767	Mm.1401	NM_009911	ENSMUSG00000045382	Cxcr4	CD184|CXC-R4|CXCR-4|Cmkar4|LESTR|PB-CKR|PBSF/SDF-1|Sdf1r|b2b220Clo	chemokine (C-X-C motif) receptor 4	protein-coding
Merged-chr10-59923134-1	chr10	59923046	59923222	+	1	NA	Intergenic	Intergenic	28636	NM_029083	74747	Mm.21697	NM_029083	ENSMUSG00000020108	Ddit4	5830413E08Rik|AA415483|REDD1|Rtp801|dig2	DNA-damage-inducible transcript 4	protein-coding
Merged-chr13-66800537-1	chr13	66800395	66800679	+	1	NA	Intergenic	Intergenic	104813	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr8-11530283-1	chr8	11530166	11530400	+	1	NA	intron (NM_001359137, intron 7 of 14)	intron (NM_001359137, intron 7 of 14)	20488	NM_001359137	71941	Mm.196576	NM_024248	ENSMUSG00000056228	Cars2	2310051N18Rik|2410044A07Rik|D530030H10Rik|cysRS	cysteinyl-tRNA synthetase 2 (mitochondrial)(putative)	protein-coding
Merged-chr15-59931678-1	chr15	59931592	59931764	+	1	NA	Intergenic	Intergenic	84940	NM_027668	71088	Mm.425950	NM_027668	ENSMUSG00000071749	4933412E24Rik	-	RIKEN cDNA 4933412E24 gene	protein-coding
Merged-chr8-71375950-1	chr8	71375851	71376050	+	1	NA	exon (NM_010150, exon 3 of 4)	exon (NM_010150, exon 3 of 4)	4652	NM_029865	77090	Mm.440170	NM_029865	ENSMUSG00000002396	Ocel1	9430098E02Rik|AI326022|AI593544	occludin/ELL domain containing 1	protein-coding
Merged-chr1-173835575-1	chr1	173835488	173835663	+	1	NA	Intergenic	L1Md_T|LINE|L1	44612	NM_001170853	100040462	Mm.463437	NM_001170853	ENSMUSG00000090272	Mndal	Gm2785|Ifi212	myeloid nuclear differentiation antigen like	protein-coding
Merged-chr1-193808044-1	chr1	193807906	193808182	+	1	NA	Intergenic	L1Md_A|LINE|L1	-300514	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
Merged-chr15-30255183-1	chr15	30255083	30255284	+	1	NA	intron (NM_001355502, intron 1 of 21)	L1Md_T|LINE|L1	82590	NM_008729	18163	Mm.321648	NM_008729	ENSMUSG00000022240	Ctnnd2	Catnd2|Nprap|neurojugin	catenin (cadherin associated protein), delta 2	protein-coding
Merged-chr14-47310957-1	chr14	47310859	47311055	+	1	NA	exon (NM_001360542, exon 3 of 4)	exon (NM_001360542, exon 3 of 4)	12683	NM_001360542	218975	Mm.212297	NM_178684	ENSMUSG00000021840	Mapk1ip1l	9130202B12|C130032J12Rik	mitogen-activated protein kinase 1 interacting protein 1-like	protein-coding
Merged-chr10-130223766-1	chr10	130223682	130223850	+	1	NA	Intergenic	L1Md_A|LINE|L1	-12638	NM_146300	258297	Mm.377419	NM_146300	ENSMUSG00000045559	Olfr827	MOR210-5	olfactory receptor 827	protein-coding
Merged-chr12-15195782-1	chr12	15195486	15196078	+	1	NA	Intergenic	L1Md_A|LINE|L1	-145393	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
Merged-chr10-41314482-1	chr10	41314190	41314775	+	1	NA	Intergenic	L1Md_T|LINE|L1	-11241	NM_133999	103199	Mm.277242	NM_133999	ENSMUSG00000038417	Fig4	A530089I17Rik|AI326867|Sac3	FIG4 phosphoinositide 5-phosphatase	protein-coding
Merged-chr1-137712484-1	chr1	137712393	137712575	+	1	NA	Intergenic	L1Md_A|LINE|L1	-253971	NR_029795	735252		NR_029795	ENSMUSG00000065565	Mir181a-1	Mirn181a-1|Mirn213|miR-213|mir-181a-1|mmu-mir-213	microRNA 181a-1	ncRNA
Merged-chr12-49056460-1	chr12	49056380	49056541	+	1	NA	Intergenic	L1Md_T|LINE|L1	-326423	NM_001160112	15228	Mm.4704	NM_008241	ENSMUSG00000020950	Foxg1	2900064B05Rik|BF-1|Bf1|Hfh9|Hfhbf1	forkhead box G1	protein-coding
Merged-chr13-8765415-1	chr13	8765280	8765551	+	1	NA	intron (NR_110345, intron 10 of 10)	MMETn-int|LTR|ERVK	105629	NM_001039389	207615	Mm.284654	NM_172445	ENSMUSG00000021147	Wdr37	-	WD repeat domain 37	protein-coding
Merged-chr5-26103549-1	chr5	26103317	26103782	+	1	NA	intron (NM_207657, intron 2 of 4)	intron (NM_207657, intron 2 of 4)	1765	NM_207657	381622	Mm.226878	NM_207657	ENSMUSG00000051940	5031410I06Rik	-	RIKEN cDNA 5031410I06 gene	protein-coding
Merged-chr1-29708938-1	chr1	29708701	29709175	+	1	NA	Intergenic	L1Md_T|LINE|L1	287450	NR_105760	102465174		NR_105760	ENSMUSG00000099257	Mir6342	Gm27268|mmu-mir-6342	microRNA 6342	ncRNA
Merged-chr5-25938766-1	chr5	25938685	25938847	+	1	NA	Intergenic	Intergenic	15578	NM_001281516	100862359		NM_001281516	ENSMUSG00000095550	Gm21671	-	predicted gene, 21671	protein-coding
Merged-chr15-78570128-1	chr15	78570039	78570217	+	1	NA	intron (NM_009008, intron 2 of 6)	L2a|LINE|L2	2655	NM_009008	19354	Mm.1972	NM_009008	ENSMUSG00000033220	Rac2	AI323801|AI452260	Rac family small GTPase 2	protein-coding
Merged-chr19-7540367-1	chr19	7540270	7540465	+	1	NA	Intergenic	RMER21B|LTR|ERV1	-17092	NM_139269	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	AdPLA|C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
Merged-chr1-84573109-1	chr1	84573021	84573197	+	1	NA	intron (NM_152915, intron 4 of 12)	L1Md_T|LINE|L1	-122730	NR_039588	100628595		NR_039588	ENSMUSG00000093254	Mir5126	mir-5126|mmu-mir-5126|mu-mir-5126	microRNA 5126	ncRNA
Merged-chr11-98849524-1	chr11	98849430	98849619	+	1	NA	intron (NM_001080925, intron 10 of 14)	intron (NM_001080925, intron 10 of 14)	12739	NM_001080925	268480	Mm.340766	NM_001080925	ENSMUSG00000038020	Rapgefl1	B230105J10	Rap guanine nucleotide exchange factor (GEF)-like 1	protein-coding
Merged-chr13-100277856-1	chr13	100277751	100277962	+	1	NA	Intergenic	Lx5b|LINE|L1	-30520	NM_010870	17951	Mm.290476	NM_010870	ENSMUSG00000071203	Naip5	Birc1e|Lgn1|Naip-rs3	NLR family, apoptosis inhibitory protein 5	protein-coding
Merged-chr10-16822737-1	chr10	16822549	16822926	+	1	NA	Intergenic	L1Md_T|LINE|L1	273045	NR_038020	100504235	Mm.84044	NR_038020	ENSMUSG00000101969	Gm20125	-	predicted gene, 20125	ncRNA
Merged-chr1-94475606-1	chr1	94475514	94475698	+	1	NA	Intergenic	L1Md_A|LINE|L1	-321836	NR_040473	74689	Mm.399187	NR_040473	ENSMUSG00000100518	4930440C22Rik	-	RIKEN cDNA 4930440C22 gene	ncRNA
Merged-chr1-193805683-1	chr1	193805454	193805913	+	1	NA	Intergenic	L1Md_A|LINE|L1	-298153	NR_029592	387201		NR_029592	ENSMUSG00000065533	Mir205	Mirn205|mir-205|mmu-mir-205	microRNA 205	ncRNA
Merged-chr15-102707912-1	chr15	102707730	102708095	+	1	NA	intron (NM_026192, intron 14 of 14)	intron (NM_026192, intron 14 of 14)	14266	NM_026192	67488	Mm.71682	NM_026192	ENSMUSG00000023055	Calcoco1	1810009B06Rik|Cocoa|Gcap11|mKIAA1536	calcium binding and coiled coil domain 1	protein-coding
Merged-chr15-64921579-1	chr15	64921382	64921776	+	1	NA	5' UTR (NM_001291903, exon 1 of 17)	5' UTR (NM_001291903, exon 1 of 17)	717	NM_009623	11514	Mm.1425	NM_009623	ENSMUSG00000022376	Adcy8	AC8|AW060868	adenylate cyclase 8	protein-coding
Merged-chr6-136402928-1	chr6	136402822	136403034	+	1	NA	intron (NM_001201390, intron 1 of 1)	intron (NM_001201390, intron 1 of 1)	12641	NM_001201390	100502936	Mm.21182	NM_001201390	ENSMUSG00000045291	E330021D16Rik	C85549	RIKEN cDNA E330021D16 gene	protein-coding
Merged-chr15-77866753-1	chr15	77866658	77866848	+	1	NA	Intergenic	Intergenic	-24578	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
Merged-chr1-26803013-1	chr1	26802921	26803106	+	1	NA	Intergenic	L1Md_T|LINE|L1	-115553	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
Merged-chr4-75925747-1	chr4	75925638	75925857	+	1	NA	Intergenic	L1Md_T|LINE|L1	418496	NM_001352629	19266	Mm.184021	NM_011211	ENSMUSG00000028399	Ptprd	1110002J03Rik|3000002J10Rik|B230219D21Rik|R-PTP-delta	protein tyrosine phosphatase, receptor type, D	protein-coding
Merged-chr13-6781128-1	chr13	6781036	6781221	+	1	NA	Intergenic	L1Md_T|LINE|L1	-132357	NM_019703	56421	Mm.273874	NM_019703	ENSMUSG00000021196	Pfkp	1200015H23Rik|9330125N24Rik|ATP-PFK|PFK-C|PFK-P	phosphofructokinase, platelet	protein-coding
Merged-chr13-66327619-1	chr13	66327473	66327765	+	1	NA	Intergenic	ORR1A3-int|LTR|ERVL-MaLR	113499	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-47439546-1	chr10	47439462	47439630	+	1	NA	Intergenic	L1Md_Gf|LINE|L1	1194797	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr17-37119826-1	chr17	37119747	37119906	+	1	NA	Intergenic	Intergenic	-7846	NM_146456	258448	Mm.377508	NM_146456	ENSMUSG00000096477	Olfr92	MOR256-29|bM573K1.4	olfactory receptor 92	protein-coding
Merged-chr5-26011876-1	chr5	26011682	26012070	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-7149	NM_001281519	100038949		NM_001281519	ENSMUSG00000091049	Gm1979	-	predicted gene 1979	protein-coding
Merged-chr13-80683733-1	chr13	80683601	80683865	+	1	NA	Intergenic	L1Md_A|LINE|L1	-199651	NR_153410	105171	Mm.423137	NM_001042591	ENSMUSG00000074794	Arrdc3	AI450344|mKIAA1376	arrestin domain containing 3	protein-coding
Merged-chr15-94337634-1	chr15	94337540	94337728	+	1	NA	intron (NM_001164785, intron 18 of 27)	intron (NM_001164785, intron 18 of 27)	66716	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
Merged-chr17-17302164-1	chr17	17302085	17302243	+	1	NA	intron (NM_001324550, intron 1 of 3)	Lx|LINE|L1	7721	NM_001324550	100862203	Mm.484235	NM_001324550		Gm6712	EG626854	predicted gene 6712	protein-coding
Merged-chr17-27250776-1	chr17	27250571	27250982	+	1	NA	Intergenic	Intergenic	-2710	NR_131118	319720	Mm.394996	NR_131118		9630028I04Rik	-	RIKEN cDNA 9630028I04 gene	ncRNA
Merged-chr15-25747417-1	chr15	25747310	25747524	+	1	NA	intron (NM_019472, intron 19 of 40)	intron (NM_019472, intron 19 of 40)	-5789	NM_001353142	17909	Mm.60590	NM_019472	ENSMUSG00000022272	Myo10	AW048724|D15Ertd600e|mKIAA0799|myosin-X	myosin X	protein-coding
Merged-chr17-63559200-1	chr17	63559117	63559284	+	1	NA	Intergenic	L1Md_T|LINE|L1	-58620	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
Merged-chr12-115615318-1	chr12	115615205	115615432	+	1	NA	Intergenic	Intergenic	80476	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr19-7482941-1	chr19	7482840	7483043	+	1	NA	exon (NM_001271487, exon 1 of 8)	exon (NM_001271487, exon 1 of 8)	350	NM_001003933	20168	Mm.246990	NM_053076	ENSMUSG00000024758	Rtn3	RTN3-A1	reticulon 3	protein-coding
Merged-chr10-35352370-1	chr10	35352285	35352455	+	1	NA	Intergenic	L1Md_A|LINE|L1	868970	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
Merged-chr8-84198057-1	chr8	84197954	84198160	+	1	NA	Intergenic	Intergenic	-10461	NR_029740	387216		NR_029740	ENSMUSG00000065611	Mir23a	Mirn23a|mir-23a|mmu-mir-23a	microRNA 23a	ncRNA
Merged-chr1-97283009-1	chr1	97282923	97283095	+	1	NA	Intergenic	L1Md_A|LINE|L1	-154706	NM_028942	74441	Mm.60362	NM_028942	ENSMUSG00000026331	Slco6c1	4933404A18Rik|C79179	solute carrier organic anion transporter family, member 6c1	protein-coding
Merged-chr15-78843118-1	chr15	78843035	78843202	+	1	NA	intron (NM_027219, intron 1 of 2)	CpG	471	NM_027219	104445	Mm.307488	NM_027219	ENSMUSG00000049521	Cdc42ep1	1810058K22Rik|AA980734|Borg5|CEP1|MSE55	CDC42 effector protein (Rho GTPase binding) 1	protein-coding
Merged-chr19-47897835-1	chr19	47897736	47897935	+	1	NA	exon (NM_001001738, exon 2 of 2)	exon (NM_001001738, exon 2 of 2)	21464	NM_001001738	414801	Mm.29457	NM_001001738	ENSMUSG00000044948	Itprip	4833424O12Rik|DANGER	inositol 1,4,5-triphosphate receptor interacting protein	protein-coding
Merged-chr19-46486543-1	chr19	46486316	46486771	+	1	NA	3' UTR (NM_015752, exon 12 of 12)	3' UTR (NM_015752, exon 12 of 12)	-15105	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
Merged-chr1-127072647-1	chr1	127072553	127072741	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-132339	NM_145128	107895	Mm.214682	NM_145128	ENSMUSG00000036155	Mgat5	4930471A21Rik|5330407H02Rik|AI480971|GlcNAc-TV	mannoside acetylglucosaminyltransferase 5	protein-coding
Merged-chr1-31080181-1	chr1	31080047	31080316	+	1	NA	intron (NR_136907, intron 1 of 3)	L1Md_T|LINE|L1	16273	NR_136907	102634473	Mm.484482	NR_136907	ENSMUSG00000100371	Gm29669	-	predicted gene 29669	ncRNA
Merged-chr10-81123289-1	chr10	81123180	81123398	+	1	NA	intron (NM_023138, intron 10 of 10)	B1_Mus2|SINE|Alu	-12982	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
Merged-chr8-27304845-1	chr8	27304739	27304952	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	8800	NR_003107	732482	Mm.463248	NR_003107		Gm9731	-	Fam58a pseudogene	pseudo
Merged-chr10-33776411-1	chr10	33776264	33776559	+	1	NA	intron (NM_001101452, intron 4 of 5)	L1Md_T|LINE|L1	5704	NM_001101452	215895	Mm.473684	NM_001101452	ENSMUSG00000090298	Sult3a2	EG215895|Gm4794	sulfotransferase family 3A, member 2	protein-coding
Merged-chr2-156720962-1	chr2	156720879	156721045	+	1	NA	promoter-TSS (NR_040505)	promoter-TSS (NR_040505)	-3	NM_001042488	228836	Mm.22094	NM_146128	ENSMUSG00000061689	Dlgap4	AI225853|BC024558|DAP-4|DAP4|SAPAP-4|Sapap4|WBP16	DLG associated protein 4	protein-coding
Merged-chr11-99829941-1	chr11	99829829	99830054	+	1	NA	Intergenic	L1Md_T|LINE|L1	8125	NM_001195383	100502865	Mm.476649	NM_001195383	ENSMUSG00000078257	2300003K06Rik	-	RIKEN cDNA 2300003K06 gene	protein-coding
Merged-chr10-76549300-1	chr10	76549203	76549398	+	1	NA	intron (NM_146006, intron 18 of 21)	intron (NM_146006, intron 18 of 21)	12926	NR_045354	74953	Mm.401971	NR_045354	ENSMUSG00000086241	4930483K19Rik	-	RIKEN cDNA 4930483K19 gene	ncRNA
Merged-chr13-66304821-1	chr13	66304689	66304954	+	1	NA	Intergenic	Intergenic	136297	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr13-64833265-1	chr13	64833152	64833378	+	1	NA	intron (NM_001081129, intron 3 of 23)	MuRRS-int|LTR|ERV1	70623	NM_001081129	238680	Mm.390590	NM_001081129	ENSMUSG00000033063	Cntnap3	-	contactin associated protein-like 3	protein-coding
Merged-chr5-29351129-1	chr5	29351032	29351226	+	1	NA	intron (NM_020295, intron 3 of 16)	L1Md_T|LINE|L1	27261	NM_020295	56873	Mm.41572	NM_020295	ENSMUSG00000010721	Lmbr1	1110048D14Rik|AU017641	limb region 1	protein-coding
Merged-chr4-88791165-1	chr4	88790987	88791343	+	1	NA	promoter-TSS (NM_001243166)	promoter-TSS (NM_001243166)	-225	NM_001243166	545653	Mm.489586	NM_001243166	ENSMUSG00000099420	Gm13279	-	predicted gene 13279	protein-coding
Merged-chr1-174710176-1	chr1	174710068	174710285	+	1	NA	intron (NM_019445, intron 13 of 17)	L1Md_A|LINE|L1	208351	NM_019445	54418	Mm.330620	NM_019445	ENSMUSG00000028354	Fmn2	AU024104	formin 2	protein-coding
Merged-chr13-66590339-1	chr13	66590141	66590538	+	1	NA	Intergenic	Intergenic	-149221	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-52891021-1	chr1	52890930	52891112	+	1	NA	intron (NM_146108, intron 7 of 13)	L1Md_A|LINE|L1	45983	NM_146108	227095	Mm.222063	NM_146108	ENSMUSG00000041426	Hibch	2610509I15Rik|HIBYL-COA-H	3-hydroxyisobutyryl-Coenzyme A hydrolase	protein-coding
Merged-chr13-77642881-1	chr13	77642730	77643033	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-65809	NM_138312	68675	Mm.343005	NM_138312	ENSMUSG00000064138	Fam172a	1110033M05Rik|2610318O14Rik|53-E6|9430037D06Rik|AF064782|pEN87	family with sequence similarity 172, member A	protein-coding
Merged-chr1-33412135-1	chr1	33412015	33412255	+	1	NA	Intergenic	L1Md_T|LINE|L1	257659	NM_008922	19076	Mm.27705	NM_008922	ENSMUSG00000026134	Prim2	AI323589	DNA primase, p58 subunit	protein-coding
Merged-chr1-129441110-1	chr1	129441004	129441217	+	1	NA	intron (NM_172485, intron 2 of 27)	L1Md_T|LINE|L1	167806	NM_172485	210417	Mm.380518	NM_172485	ENSMUSG00000042581	Thsd7b	1700074E13Rik|B930082A18|D130067I03Rik	thrombospondin, type I, domain containing 7B	protein-coding
Merged-chr11-25560459-1	chr11	25560316	25560602	+	1	NA	Intergenic	L1Md_A|LINE|L1	234352	NR_045853	71234	Mm.158627	NR_045853	ENSMUSG00000033015	4933427E13Rik	-	RIKEN cDNA 4933427E13 gene	ncRNA
Merged-chr7-10008539-1	chr7	10008368	10008710	+	1	NA	Intergenic	Intergenic	-16400	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr2-173898964-1	chr2	173898875	173899054	+	1	NA	Intergenic	Lx7|LINE|L1	161393	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
Merged-chr15-40318229-1	chr15	40318142	40318317	+	1	NA	Intergenic	L1Md_F2|LINE|L1	155622	NR_155349	102636151	Mm.321976	NR_155349	ENSMUSG00000115367	Gm33301	-	predicted gene, 33301	ncRNA
Merged-chr15-86185664-1	chr15	86185498	86185831	+	1	NA	promoter-TSS (NR_155352)	promoter-TSS (NR_155352)	-64	NR_155352	102638208	Mm.415090	NR_155352	ENSMUSG00000086424	Gm15569	-	predicted gene 15569	ncRNA
Merged-chr13-67931323-1	chr13	67931243	67931404	+	1	NA	Intergenic	(CAGA)n|Simple_repeat|Simple_repeat	67997	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr13-92344929-1	chr13	92344848	92345010	+	1	NA	intron (NM_001311120, intron 7 of 23)	intron (NM_001311120, intron 7 of 23)	-9854	NM_010049	13361	Mm.23695	NM_010049	ENSMUSG00000021707	Dhfr	8430436I03Rik|AA607882|AI662710|AW555094	dihydrofolate reductase	protein-coding
Merged-chr1-19690314-1	chr1	19690138	19690491	+	1	NA	Intergenic	L1Md_A|LINE|L1	478260	NM_001025305	21419	Mm.137021	NM_009334	ENSMUSG00000025927	Tfap2b	AI606113|AP-2(beta)|E130018K07Rik|Tcfap2b	transcription factor AP-2 beta	protein-coding
Merged-chr17-35017052-1	chr17	35016945	35017159	+	1	NA	TTS (NM_011690)	TTS (NM_011690)	473	NM_001347347	27762	Mm.56895	NM_138582	ENSMUSG00000007030	Vwa7	C6orf27|D17H6S56E-3|G7c|NG37	von Willebrand factor A domain containing 7	protein-coding
Merged-chr13-68027957-1	chr13	68027854	68028061	+	1	NA	Intergenic	Intergenic	164631	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr1-84125230-1	chr1	84125120	84125341	+	1	NA	intron (NM_001003948, intron 2 of 2)	L1Md_A|LINE|L1	93731	NR_105771	102465181		NR_105771	ENSMUSG00000098851	Mir6353	Gm27391|mmu-mir-6353	microRNA 6353	ncRNA
Merged-chr1-131685867-1	chr1	131685741	131685993	+	1	NA	Intergenic	L1Md_T|LINE|L1	-2828	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
Merged-chr1-108322669-1	chr1	108322584	108322755	+	1	NA	Intergenic	L1Md_T|LINE|L1	405410	NR_102306	319596	Mm.136054	NR_102306	ENSMUSG00000100457	D830032E09Rik	-	RIKEN cDNA D830032E09 gene	ncRNA
Merged-chr10-23473635-1	chr10	23473454	23473817	+	1	NA	Intergenic	L1Md_T|LINE|L1	-123692	NM_010167	14051	Mm.332128	NM_010167	ENSMUSG00000010461	Eya4	B130023L16Rik	EYA transcriptional coactivator and phosphatase 4	protein-coding
Merged-chr1-99350317-1	chr1	99350221	99350413	+	1	NA	Intergenic	L1Md_A|LINE|L1	-422448	NM_172851	241175	Mm.251301	NM_172851	ENSMUSG00000067028	Cntnap5b	C230078M14Rik|Caspr5-2	contactin associated protein-like 5B	protein-coding
Merged-chr4-93707448-1	chr4	93707331	93707565	+	1	NA	Intergenic	L1Md_T|LINE|L1	-371937	NM_026954	69136	Mm.171558	NM_026954	ENSMUSG00000054000	Tusc1	2200001D17Rik|TSG-9	tumor suppressor candidate 1	protein-coding
Merged-chr17-23294121-1	chr17	23293916	23294327	+	1	NA	intron (NM_001102584, intron 5 of 5)	L1_Mus4|LINE|L1	18192	NM_001102584	666002	Mm.469838	NM_001102584	ENSMUSG00000091945	Vmn2r114	EG666002|V2Rp3	vomeronasal 2, receptor 114	protein-coding
Merged-chr12-115620589-1	chr12	115620426	115620752	+	1	NA	Intergenic	L1Md_F2|LINE|L1	75205	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr1-140046275-1	chr1	140046063	140046487	+	1	NA	Intergenic	L1Md_T|LINE|L1	137136	NM_009888	12628	Mm.8655	NM_009888	ENSMUSG00000026365	Cfh	Mud-1|NOM|Sas-1|Sas1	complement component factor h	protein-coding
Merged-chr10-51347955-1	chr10	51347870	51348041	+	1	NA	Intergenic	L1Md_A|LINE|L1	-132657	NM_008147	14727	Mm.439661	NM_008147	ENSMUSG00000112023	Lilr4b	Gp49a|gp49	leukocyte immunoglobulin-like receptor, subfamily B, member 4B	protein-coding
Merged-chr12-74927457-1	chr12	74927369	74927546	+	1	NA	intron (NM_172805, intron 10 of 10)	L1Md_T|LINE|L1	249875	NM_172805	238271	Mm.44465	NM_172805	ENSMUSG00000034402	Kcnh5	Eag2	potassium voltage-gated channel, subfamily H (eag-related), member 5	protein-coding
Merged-chr10-10976904-1	chr10	10976779	10977030	+	1	NA	intron (NM_001114333, intron 2 of 9)	L1Md_T|LINE|L1	105427	NM_016976	14816	Mm.391904	NM_016976	ENSMUSG00000019828	Grm1	4930455H15Rik|Gm10828|Gprc1a|mGluR1|nmf373|rcw|wobl	glutamate receptor, metabotropic 1	protein-coding
Merged-chr12-108573748-1	chr12	108573617	108573880	+	1	NA	intron (NM_001163394, intron 1 of 13)	L1Md_T|LINE|L1	-18130	NR_045751	100504467	Mm.394980	NR_045751		Gm16596	-	predicted gene, 16596	ncRNA
Merged-chr10-54717153-1	chr10	54717067	54717240	+	1	NA	Intergenic	L1Md_A|LINE|L1	641231	NR_038016	100502920	Mm.403982	NR_038016	ENSMUSG00000097069	Gm16998	-	predicted gene, 16998	ncRNA
Merged-chr1-17388563-1	chr1	17388428	17388699	+	1	NA	Intergenic	L1Md_T|LINE|L1	-213338	NM_053191	94227	Mm.442452	NM_053191	ENSMUSG00000067780	Pi15	P24TI|P25TI|PI-15|SugarCrisp	peptidase inhibitor 15	protein-coding
Merged-chr11-13382332-1	chr11	13382233	13382431	+	1	NA	Intergenic	L1Md_T|LINE|L1	796709	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr14-120062267-1	chr14	120062179	120062355	+	1	NA	Intergenic	L1Md_T|LINE|L1	-19832	NM_001001490	239283	Mm.138520	NM_001001490	ENSMUSG00000044819	Oxgr1	Cysltr3|Gm299|Gpr80|Gpr99|P2Y15	oxoglutarate (alpha-ketoglutarate) receptor 1	protein-coding
Merged-chr13-66438764-1	chr13	66438643	66438886	+	1	NA	intron (NM_001290196, intron 1 of 3)	intron (NM_001290196, intron 1 of 3)	2354	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr13-98012918-1	chr13	98012819	98013017	+	1	NA	intron (NM_012026, intron 9 of 35)	intron (NM_012026, intron 9 of 35)	193247	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
Merged-chr11-92600780-1	chr11	92600657	92600903	+	1	NA	Intergenic	L1Md_A|LINE|L1	-497586	NM_001361707	72605	Mm.342160	NM_028296	ENSMUSG00000056158	Car10	2700029L05Rik|BB085816|Ca10	carbonic anhydrase 10	protein-coding
Merged-chr1-76462689-1	chr1	76462593	76462785	+	1	NA	Intergenic	L1Md_T|LINE|L1	-26444	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA
Merged-chr1-144068247-1	chr1	144068055	144068440	+	1	NA	Intergenic	L1Md_A|LINE|L1	-64098	NM_009061	19735	Mm.28262	NM_009061	ENSMUSG00000026360	Rgs2	GOS8	regulator of G-protein signaling 2	protein-coding
Merged-chr15-73985661-1	chr15	73985572	73985750	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	-145990	NM_001033365	268816	Mm.440635	NM_001033365	ENSMUSG00000072487	Mroh5	Gm628	maestro heat-like repeat family member 5	protein-coding
Merged-chr13-62115347-1	chr13	62115263	62115432	+	1	NA	Intergenic	Intergenic	-14543	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr12-61704192-1	chr12	61704057	61704327	+	1	NA	intron (NM_001310586, intron 2 of 5)	L1Md_T|LINE|L1	181025	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
Merged-chr11-11143051-1	chr11	11142894	11143208	+	1	NA	intron (NM_177033, intron 2 of 3)	L1Md_T|LINE|L1	29035	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr15-50060304-1	chr15	50060208	50060400	+	1	NA	Intergenic	L1Md_A|LINE|L1	828745	NM_001310481	83925	Mm.30466	NM_032000	ENSMUSG00000038679	Trps1	AI115454|AI447310|D15Ertd586e	transcriptional repressor GATA binding 1	protein-coding
Merged-chr19-55964630-1	chr19	55964550	55964711	+	1	NA	Intergenic	Intergenic	69309	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
Merged-chr1-78949351-1	chr1	78949226	78949477	+	1	NA	intron (NR_151519, intron 2 of 3)	L1Md_A|LINE|L1	132440	NM_021342	57814	Mm.24386	NM_021342	ENSMUSG00000047330	Kcne4	AW487937|MiRP3	potassium voltage-gated channel, Isk-related subfamily, gene 4	protein-coding
Merged-chr12-6015074-1	chr12	6014969	6015180	+	1	NA	Intergenic	L1Md_A|LINE|L1	638572	NR_015579	72669	Mm.10434	NM_028318		2810032G03Rik	AI461720	RIKEN cDNA 2810032G03 gene	ncRNA
Merged-chr1-109036010-1	chr1	109035884	109036136	+	1	NA	Intergenic	L1Md_T|LINE|L1	-946890	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr15-78406775-1	chr15	78406691	78406859	+	1	NA	promoter-TSS (NM_001162493)	promoter-TSS (NM_001162493)	-26	NM_001162492	246221	Mm.294215	NM_138670	ENSMUSG00000071711	Mpst	Mst	mercaptopyruvate sulfurtransferase	protein-coding
Merged-chr7-88783650-1	chr7	88783561	88783740	+	1	NA	Intergenic	L1Md_T|LINE|L1	353377	NM_028238	72433	Mm.276669	NM_028238	ENSMUSG00000030559	Rab38	2310011F14Rik|AU043391|cht	RAB38, member RAS oncogene family	protein-coding
Merged-chr13-66725463-1	chr13	66725198	66725728	+	1	NA	Intergenic	MT2B1|LTR|ERVL	179887	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr1-140925824-1	chr1	140925720	140925928	+	1	NA	Intergenic	L1Md_T|LINE|L1	-269422	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr1-50334635-1	chr1	50334471	50334800	+	1	NA	Intergenic	L1Md_T|LINE|L1	-592888	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
Merged-chr12-115296014-1	chr12	115295922	115296106	+	1	NA	Intergenic	Intergenic	399780	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr13-66727264-1	chr13	66727186	66727343	+	1	NA	Intergenic	RLTR18B|LTR|ERVK	178086	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr5-6184966-1	chr5	6184841	6185092	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-435649	NM_027399	70358	Mm.85429	NM_027399	ENSMUSG00000015652	Steap1	2410007B19Rik|Prss24|Steap	six transmembrane epithelial antigen of the prostate 1	protein-coding
Merged-chr1-140647769-1	chr1	140647570	140647968	+	1	NA	intron (NR_040604, intron 1 of 3)	L1Md_T|LINE|L1	8633	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr5-92646511-1	chr5	92646417	92646605	+	1	NA	intron (NM_001360018, intron 12 of 24)	G-rich|Low_complexity|Low_complexity	28616	NM_001360018	320696	Mm.209991	NM_177230	ENSMUSG00000050050	Ccdc158	4932413O14Rik	coiled-coil domain containing 158	protein-coding
Merged-chr9-9545012-1	chr9	9544913	9545112	+	1	NA	Intergenic	L1Md_T|LINE|L1	-305999	NM_027823	71544	Mm.334955	NM_027823	ENSMUSG00000050730	Arhgap42	9030420J04Rik|BE136619	Rho GTPase activating protein 42	protein-coding
Merged-chr12-14454416-1	chr12	14454314	14454518	+	1	NA	Intergenic	L1Md_T|LINE|L1	192882	NR_045003	791361	Mm.217963	NR_045003	ENSMUSG00000113336	Gm16497	-	predicted gene 16497	ncRNA
Merged-chr8-120495062-1	chr8	120494962	120495163	+	1	NA	intron (NM_198671, intron 1 of 15)	intron (NM_198671, intron 1 of 15)	6196	NM_198671	382034	Mm.334856	NM_198671	ENSMUSG00000031822	Gse1	2210013I18Rik|mKIAA0182	genetic suppressor element 1, coiled-coil protein	protein-coding
Merged-chr11-45101122-1	chr11	45100980	45101264	+	1	NA	Intergenic	L1Md_T|LINE|L1	15806	NR_045100	100504255	Mm.123608	NR_045100	ENSMUSG00000084773	Gm12159	-	predicted gene 12159	ncRNA
Merged-chr3-92548225-1	chr3	92548110	92548341	+	1	NA	Intergenic	L1Md_A|LINE|L1	25510	NM_008412	16447	Mm.207365	NM_008412	ENSMUSG00000049128	Ivl	1110019C06Rik	involucrin	protein-coding
Merged-chr15-75963388-1	chr15	75963258	75963519	+	1	NA	Intergenic	Intergenic	-5735	NM_001347040	69020	Mm.294295	NM_001081065	ENSMUSG00000034429	Zfp707	1500031N24Rik|AI451708|AW495315	zinc finger protein 707	protein-coding
Merged-chr19-46481755-1	chr19	46481577	46481933	+	1	NA	intron (NM_001025391, intron 10 of 11)	intron (NM_001025391, intron 10 of 11)	-19893	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
Merged-chr5-26054116-1	chr5	26054028	26054205	+	1	NA	Intergenic	Intergenic	-14611	NM_029376	75657	Mm.374273	NM_029376	ENSMUSG00000073119	Speer4a	1700027N01Rik|SPEER-4A	spermatogenesis associated glutamate (E)-rich protein 4A	protein-coding
Merged-chr8-20996167-1	chr8	20995884	20996451	+	1	NA	Intergenic	RMER19B|LTR|ERVK	-29378	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr1-63832252-1	chr1	63832167	63832338	+	1	NA	Intergenic	L1Md_A|LINE|L1	-62985	NM_001256158	74426	Mm.159197	NM_001256158	ENSMUSG00000025961	4933402D24Rik	-	RIKEN cDNA 4933402D24 gene	protein-coding
Merged-chr19-11673791-1	chr19	11673691	11673892	+	1	NA	intron (NM_133353, intron 3 of 4)	L1Md_F2|LINE|L1	-13232	NM_001037634	225922	Mm.26881	NM_001037634	ENSMUSG00000055895	Oosp2	Gm99|Plac1l|Tmem122	oocyte secreted protein 2	protein-coding
Merged-chr17-22620595-1	chr17	22620484	22620706	+	1	NA	Intergenic	L1Md_F2|LINE|L1	19447	NM_001104575	628185	Mm.390947	NM_001104575	ENSMUSG00000094921	Vmn2r112	EG628185|V2rp1	vomeronasal 2, receptor 112	protein-coding
Merged-chrX-161712354-1	chrX	161712213	161712495	+	1	NA	Intergenic	L1Md_A|LINE|L1	-4682	NM_001103367	24004	Mm.328503	NM_198409	ENSMUSG00000043518	Rai2	3f8	retinoic acid induced 2	protein-coding
Merged-chr1-141193915-1	chr1	141193817	141194014	+	1	NA	Intergenic	L1Md_T|LINE|L1	-537513	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr13-68346901-1	chr13	68346794	68347009	+	1	NA	Intergenic	B4|SINE|B4	9924	NR_152173	666272	Mm.309128	NR_152173	ENSMUSG00000113050	Gm8016	EG666272	predicted gene 8016	ncRNA
Merged-chr1-13549734-1	chr1	13549642	13549826	+	1	NA	Intergenic	L1Md_T|LINE|L1	40176	NM_028173	72265	Mm.28765	NM_028173	ENSMUSG00000025935	Tram1	1810049E02Rik|TRAMP	translocating chain-associating membrane protein 1	protein-coding
Merged-chr13-62560430-1	chr13	62560330	62560531	+	1	NA	Intergenic	Intergenic	-1801	NM_001360915	77117	Mm.440905	NM_175252	ENSMUSG00000074865	Zfp934	6720457D02Rik	zinc finger protein 934	protein-coding
Merged-chr16-36298990-1	chr16	36298849	36299131	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	21842	NM_001082543	20861	Mm.327618	NM_001082543	ENSMUSG00000071562	Stfa1	Stefin-3|Stf-3|Stf1|Stf3|Stfa3	stefin A1	protein-coding
Merged-chr15-98168645-1	chr15	98168559	98168732	+	1	NA	exon (NM_177716, exon 1 of 1)	exon (NM_177716, exon 1 of 1)	839	NM_177716	239650	Mm.54140	NM_177716	ENSMUSG00000029875	Ccdc184	5630400A08|AI836003	coiled-coil domain containing 184	protein-coding
Merged-chr5-77406416-1	chr5	77406270	77406562	+	1	NA	intron (NM_001159518, intron 1 of 5)	intron (NM_001159518, intron 1 of 5)	1629	NM_001159518	29817	Mm.233470	NM_008048	ENSMUSG00000036256	Igfbp7	AGM|Fstl2|Mac25	insulin-like growth factor binding protein 7	protein-coding
Merged-chr10-81417700-1	chr10	81417606	81417794	+	1	NA	intron (NM_026756, intron 2 of 8)	intron (NM_026756, intron 2 of 8)	-1403	NR_106141	102465778		NR_106141	ENSMUSG00000105379	Mir1191b	mmu-mir-1191b	microRNA 1191b	ncRNA
Merged-chr1-96193223-1	chr1	96193075	96193372	+	1	NA	Intergenic	Lx|LINE|L1	-171465	NR_040467	73454	Mm.396229	NR_040467	ENSMUSG00000100062	1700063A18Rik	-	RIKEN cDNA 1700063A18 gene	ncRNA
Merged-chr1-32671694-1	chr1	32671545	32671844	+	1	NA	Intergenic	L1Md_T|LINE|L1	-124401	NM_001164286	408191	Mm.479439	NM_001164286	ENSMUSG00000091318	Gm5415	EG408191|Senp14	predicted gene 5415	protein-coding
Merged-chr8-126895226-1	chr8	126895121	126895332	+	1	NA	Intergenic	Intergenic	46206	NR_151740	414091	Mm.240068	NM_001033546		A630001O12Rik	Gm45803	RIKEN cDNA A630001O12 gene	ncRNA
Merged-chr11-74369758-1	chr11	74369625	74369891	+	1	NA	Intergenic	Intergenic	5087	NM_001011851	258153	Mm.376124	NM_001011851	ENSMUSG00000058275	Olfr412	MOR127-5P	olfactory receptor 412	protein-coding
Merged-chr1-148462791-1	chr1	148462694	148462888	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	1459648	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr10-79927520-1	chr10	79927424	79927616	+	1	NA	intron (NM_001288625, intron 1 of 8)	CpG	179	NM_001288625	13496	Mm.301282	NM_007880	ENSMUSG00000019564	Arid3a	Bright|Dri1|Dril1	AT rich interactive domain 3A (BRIGHT-like)	protein-coding
Merged-chr1-113056752-1	chr1	113056661	113056844	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1191834	NM_001081316	319901	Mm.103468	NM_001081316	ENSMUSG00000038702	Dsel	9330132E09Rik|DS-epi2	dermatan sulfate epimerase-like	protein-coding
Merged-chr13-55487498-1	chr13	55487420	55487576	+	1	NA	intron (NM_001177371, intron 1 of 14)	CpG	578	NM_001177372	56320	Mm.19016	NM_019813	ENSMUSG00000034675	Dbn1	-	drebrin 1	protein-coding
Merged-chr1-25595394-1	chr1	25595240	25595549	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	234313	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr13-68279587-1	chr13	68279420	68279754	+	1	NA	Intergenic	B4|SINE|B4	-44856	NR_155295	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr19-7560093-1	chr19	7559953	7560234	+	1	NA	intron (NM_001362425, intron 2 of 4)	intron (NM_001362425, intron 2 of 4)	2608	NM_001362425	225845	Mm.274810	NM_139269	ENSMUSG00000060675	Pla2g16	AdPLA|C78643|HRSL3|Hrasls3|Hrev107|MLP-3	phospholipase A2, group XVI	protein-coding
Merged-chr13-66446724-1	chr13	66446616	66446832	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-5606	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr15-96948411-1	chr15	96948234	96948589	+	1	NA	Intergenic	RMER1A|Other|Other	71948	NM_001358059	69354	Mm.250980	NM_027052	ENSMUSG00000022464	Slc38a4	1110012E16Rik|1700012A18Rik|Ata3|mATA3|mNAT3	solute carrier family 38, member 4	protein-coding
Merged-chr15-86216821-1	chr15	86216727	86216915	+	1	NA	intron (NM_145476, intron 1 of 12)	intron (NM_145476, intron 1 of 12)	2362	NM_145476	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
Merged-chr1-122421529-1	chr1	122421416	122421642	+	1	NA	Intergenic	L1Md_A|LINE|L1	216384	NR_151524	102638832	Mm.112794	NR_151524	ENSMUSG00000099960	Gm28590	-	predicted gene 28590	ncRNA
Merged-chr10-27258364-1	chr10	27258237	27258491	+	1	NA	intron (NM_008481, intron 14 of 63)	L1Md_T|LINE|L1	-131502	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
Merged-chr11-27383192-1	chr11	27383032	27383352	+	1	NA	Intergenic	L1Md_T|LINE|L1	598084	NR_002890	654472	Mm.347777	NR_002890		Gm12070	-	glyceraldehyde-3-phosphate dehydrogenase pseudogene	pseudo
Merged-chr15-5242458-1	chr15	5242332	5242585	+	1	NA	exon (NM_008965, exon 2 of 3)	exon (NM_008965, exon 2 of 3)	1729	NM_001136079	19219	Mm.18509	NM_008965	ENSMUSG00000039942	Ptger4	EP4|Ptgerep4	prostaglandin E receptor 4 (subtype EP4)	protein-coding
Merged-chr16-64994098-1	chr16	64994020	64994177	+	1	NA	intron (NM_008310, intron 2 of 2)	L1Md_T|LINE|L1	111686	NM_008310	15557	Mm.5040	NM_008310	ENSMUSG00000050783	Htr1f	Htr1eb	5-hydroxytryptamine (serotonin) receptor 1F	protein-coding
Merged-chr11-118385615-1	chr11	118385496	118385734	+	1	NA	Intergenic	L1Md_F2|LINE|L1	16344	NM_011150	19039	Mm.3152	NM_011150	ENSMUSG00000033880	Lgals3bp	90K|CyCAP|MAC-2BP|Ppicap|Tango10b	lectin, galactoside-binding, soluble, 3 binding protein	protein-coding
Merged-chr15-77609943-1	chr15	77609842	77610044	+	1	NA	Intergenic	RMER17A|LTR|ERVK	-13818	NM_177820	328561	Mm.379486	NM_177820	ENSMUSG00000050014	Apol10b	9130218O11Rik	apolipoprotein L 10B	protein-coding
Merged-chr7-30933631-1	chr7	30933520	30933742	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-9450	NM_183257	66438	Mm.389860	NM_183257	ENSMUSG00000056978	Hamp2	1810073K19Rik|HEPC2	hepcidin antimicrobial peptide 2	protein-coding
Merged-chr15-74730957-1	chr15	74730876	74731039	+	1	NA	Intergenic	(TGGA)n|Simple_repeat|Simple_repeat	-2931	NM_020519	57277	Mm.27630	NM_020519	ENSMUSG00000022596	Slurp1	1110021N19Rik|AI415082|ARS|ArsB|Slurp-1	secreted Ly6/Plaur domain containing 1	protein-coding
Merged-chr3-32140046-1	chr3	32139854	32140238	+	1	NA	intron (NM_028231, intron 2 of 5)	MTA_Mm-int|LTR|ERVL-MaLR	-225443	NR_027966	67576	Mm.435324	NR_027966		4930429B21Rik	-	RIKEN cDNA 4930429B21 gene	ncRNA
Merged-chr19-29179546-1	chr19	29179454	29179639	+	1	NA	Intergenic	Intergenic	44267	NR_029778	724062		NR_029778	ENSMUSG00000065556	Mir101b	Mirn101b|mir-101b	microRNA 101b	ncRNA
Merged-chr10-32969238-1	chr10	32969051	32969425	+	1	NA	Intergenic	L1Md_T|LINE|L1	-79323	NM_001025286	432450	Mm.49665	NM_001013411	ENSMUSG00000069670	Nkain2	6330571D19Rik|AW455467|Tcba1	Na+/K+ transporting ATPase interacting 2	protein-coding
Merged-chr19-47068496-1	chr19	47068400	47068592	+	1	NA	intron (NM_177342, intron 1 of 10)	intron (NM_177342, intron 1 of 10)	748	NM_177342	226182	Mm.301522	NM_177342	ENSMUSG00000025049	Taf5	6330528C20Rik|AV117817	TATA-box binding protein associated factor 5	protein-coding
Merged-chr13-3964519-1	chr13	3964434	3964605	+	1	NA	Intergenic	(TCTCTG)n|Simple_repeat|Simple_repeat	-19170	NM_031250	83428	Mm.313662	NM_031250	ENSMUSG00000044988	Ucn3	ucn III	urocortin 3	protein-coding
Merged-chr15-75668902-1	chr15	75668803	75669002	+	1	NA	intron (NM_028404, intron 5 of 13)	intron (NM_028404, intron 5 of 13)	9898	NM_001355589	72960	Mm.182401	NM_028404	ENSMUSG00000000934	Top1mt	2900052H09Rik	DNA topoisomerase 1, mitochondrial	protein-coding
Merged-chr1-48422530-1	chr1	48422450	48422611	+	1	NA	Intergenic	L1Md_A|LINE|L1	-822086	NR_151585	442837	Mm.337149	NM_001002792	ENSMUSG00000051616	C230029F24Rik	-	RIKEN cDNA C230029F24 gene	ncRNA
Merged-chr12-115589600-1	chr12	115589509	115589692	+	1	NA	Intergenic	Intergenic	106194	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr12-41778019-1	chr12	41777937	41778101	+	1	NA	intron (NM_053122, intron 6 of 6)	L1Md_T|LINE|L1	-291962	NM_001271708	16981	Mm.404786	NM_010733	ENSMUSG00000036295	Lrrn3	NLRR-3	leucine rich repeat protein 3, neuronal	protein-coding
Merged-chr1-163789619-1	chr1	163789407	163789831	+	1	NA	intron (NM_001305643, intron 2 of 19)	L1Md_T|LINE|L1	10036	NM_010629	16579	Mm.4651	NM_010629	ENSMUSG00000026585	Kifap3	KAP-3|KAP3|SMAP	kinesin-associated protein 3	protein-coding
Merged-chr15-3217940-1	chr15	3217861	3218019	+	1	NA	Intergenic	Intergenic	-52827	NM_001042613	20363	Mm.392203	NM_009155	ENSMUSG00000064373	Selenop	AU018766|D15Ucla1|Se-P|Sepp1|selp	selenoprotein P	protein-coding
Merged-chr15-44910188-1	chr15	44910004	44910373	+	1	NA	Intergenic	LTRIS2|LTR|ERV1	28794	NR_033609	239410	Mm.352401	NR_033609	ENSMUSG00000060530	A930017M01Rik	Gm305	Smg-5 homolog, nonsense mediated mRNA decay factor pseudogene	pseudo
Merged-chr13-66802364-1	chr13	66802246	66802482	+	1	NA	Intergenic	Intergenic	102986	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr10-82390359-1	chr10	82390280	82390438	+	1	NA	Intergenic	L1Md_T|LINE|L1	102259	NM_001255990	432480	Mm.280394	NM_001255990	ENSMUSG00000094186	Gm1553	Lcrn	predicted gene 1553	protein-coding
Merged-chr10-112509028-1	chr10	112508935	112509122	+	1	NA	Intergenic	L1Md_A|LINE|L1	-217898	NR_040579	69355	Mm.84337	NR_040579	ENSMUSG00000100314	1700010J16Rik	-	RIKEN cDNA 1700010J16 gene	ncRNA
Merged-chr5-105367418-1	chr5	105367327	105367510	+	1	NA	Intergenic	RLTR13A2|LTR|ERVK	-20942	NR_132129	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
Merged-chr10-79755239-1	chr10	79755109	79755369	+	1	NA	exon (NM_023304, exon 1 of 3)	exon (NM_023304, exon 1 of 3)	120	NM_023304	67112	Mm.154211	NM_023304	ENSMUSG00000020327	Fgf22	2210414E06Rik|FGF-22	fibroblast growth factor 22	protein-coding
Merged-chr5-124425443-1	chr5	124425257	124425630	+	1	NA	intron (NM_001081203, intron 1 of 31)	CpG	159	NM_001359979	243272	Mm.23879	NM_145631	ENSMUSG00000038095	Sbno1	9330180L10Rik|AI849128|AW557836|BC021875|Sbno|mSno1|sno	strawberry notch 1	protein-coding
Merged-chr1-106852216-1	chr1	106851904	106852528	+	1	NA	Intergenic	L1Md_T|LINE|L1	-8959	NM_001360853	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
Merged-chr9-38964077-1	chr9	38963989	38964165	+	1	NA	Intergenic	L1Md_T|LINE|L1	-11601	NM_146441	258433	Mm.271361	NM_146441	ENSMUSG00000058515	Olfr933	MOR171-22	olfactory receptor 933	protein-coding
Merged-chr10-6657779-1	chr10	6657688	6657871	+	1	NA	Intergenic	L1Md_A|LINE|L1	-100814	NM_001302796	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
Merged-chr3-4305920-1	chr3	4305798	4306042	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	-492788	NR_045272	100503859	Mm.75172	NR_045272	ENSMUSG00000098659	1110015O18Rik	-	RIKEN cDNA 1110015O18 gene	ncRNA
Merged-chr11-37752979-1	chr11	37752893	37753065	+	1	NA	Intergenic	L1Md_T|LINE|L1	93990	NR_131154	100039148	Mm.120467	NR_131154	ENSMUSG00000087388	Gm12128	-	predicted gene 12128	ncRNA
Merged-chr5-146481245-1	chr5	146481093	146481398	+	1	NA	promoter-TSS (NM_001243104)	promoter-TSS (NM_001243104)	-698	NM_001243104	623198	Mm.489582	NM_001243104	ENSMUSG00000096344	Gm6408	-	predicted gene 6408	protein-coding
Merged-chr13-66309700-1	chr13	66309570	66309831	+	1	NA	Intergenic	Intergenic	131418	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr3-133402190-1	chr3	133402079	133402301	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	92080	NM_001293641	74776	Mm.210305	NM_146141	ENSMUSG00000028013	Ppa2	1110013G13Rik|Sid6306	pyrophosphatase (inorganic) 2	protein-coding
Merged-chr15-49232452-1	chr15	49232356	49232548	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-440463	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
Merged-chrX-107453383-1	chrX	107453297	107453469	+	1	NA	Intergenic	L1_Mus1|LINE|L1	-50023	NM_008409	16431	Mm.193	NM_008409	ENSMUSG00000031239	Itm2a	AW108051|Bricd2a|E25|Itm2	integral membrane protein 2A	protein-coding
Merged-chr1-168722456-1	chr1	168722377	168722535	+	1	NA	Intergenic	L1Md_T|LINE|L1	231813	NR_105766	102465178		NR_105766	ENSMUSG00000098407	Mir6348	Gm27412|mmu-mir-6348	microRNA 6348	ncRNA
Merged-chr12-115604074-1	chr12	115603942	115604206	+	1	NA	Intergenic	Intergenic	91720	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr11-9744237-1	chr11	9744138	9744337	+	1	NA	Intergenic	L1Md_A|LINE|L1	552295	NM_178259	268379	Mm.39270	NM_178259	ENSMUSG00000004668	Abca13	9830132L24|A930002G16Rik|AI956815	ATP-binding cassette, sub-family A (ABC1), member 13	protein-coding
Merged-chr13-66421815-1	chr13	66421690	66421941	+	1	NA	intron (NM_183119, intron 3 of 4)	L1_Mus2|LINE|L1	19303	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr10-115538853-1	chr10	115538729	115538977	+	1	NA	intron (NM_010195, intron 1 of 17)	L1Md_A|LINE|L1	-31133	NM_029982	77798	Mm.446685	NM_029982	ENSMUSG00000092210	A930009A15Rik	-	RIKEN cDNA A930009A15 gene	protein-coding
Merged-chr15-25218150-1	chr15	25218062	25218239	+	1	NA	Intergenic	Intergenic	195614	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
Merged-chr8-110136539-1	chr8	110136374	110136704	+	1	NA	Intergenic	(TG)n|Simple_repeat|Simple_repeat	31667	NM_007586	12308	Mm.2755	NM_007586	ENSMUSG00000003657	Calb2	CR	calbindin 2	protein-coding
Merged-chr11-84308755-1	chr11	84308677	84308833	+	1	NA	intron (NM_133360, intron 34 of 53)	L1Md_A|LINE|L1	113317	NM_133360	107476	Mm.31374	NM_133360	ENSMUSG00000020532	Acaca	A530025K05Rik|Acac|Acc1|Gm738	acetyl-Coenzyme A carboxylase alpha	protein-coding
Merged-chr15-49176902-1	chr15	49176819	49176986	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-384913	NM_001081391	239420	Mm.309363	NM_001081391	ENSMUSG00000022311	Csmd3	4930500N14Rik|mKIAA1894	CUB and Sushi multiple domains 3	protein-coding
Merged-chr13-66667277-1	chr13	66667189	66667365	+	1	NA	Intergenic	ORR1B1-int|LTR|ERVL-MaLR	-226159	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr4-53804548-1	chr4	53804468	53804629	+	1	NA	Intergenic	IAPEY3-int|LTR|ERVK	-21497	NM_028053	52076	Mm.27184	NM_028053	ENSMUSG00000028420	Tmem38b	1600017F22Rik|AA437809|AV051057|D4Ertd89e|TRIC-B|mg33b	transmembrane protein 38B	protein-coding
Merged-chr8-72076125-1	chr8	72075916	72076335	+	1	NA	Intergenic	RMER19B|LTR|ERVK	18465	NM_207555	404315	Mm.377936	NM_207555	ENSMUSG00000069998	Olfr372	MOR282-1	olfactory receptor 372	protein-coding
Merged-chr13-66541134-1	chr13	66541055	66541213	+	1	NA	Intergenic	ORR1A3-int|LTR|ERVL-MaLR	-100016	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr1-103113636-1	chr1	103113528	103113745	+	1	NA	Intergenic	L1Md_A|LINE|L1	-1654884	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr7-7509175-1	chr7	7509086	7509265	+	1	NA	Intergenic	Lx2|LINE|L1	-29202	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr11-35010355-1	chr11	35010211	35010499	+	1	NA	Intergenic	Intergenic	-111101	NM_011412	20564	Mm.478604	NM_011412	ENSMUSG00000056427	Slit3	Slil2|Slit1|b2b2362.1Clo	slit guidance ligand 3	protein-coding
Merged-chr1-109876520-1	chr1	109876440	109876600	+	1	NA	Intergenic	L1Md_T|LINE|L1	-106380	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr13-63020477-1	chr13	63020392	63020562	+	1	NA	intron (NM_001289926, intron 2 of 15)	L1Md_T|LINE|L1	55584	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
Merged-chr19-46357022-1	chr19	46356929	46357115	+	1	NA	intron (NM_029186, intron 1 of 8)	CpG	142	NM_029186	75146	Mm.159290	NM_029186	ENSMUSG00000025227	Mfsd13a	4930449A08Rik|4930538D17Rik|Tmem180	major facilitator superfamily domain containing 13a	protein-coding
Merged-chr1-158335972-1	chr1	158335829	158336115	+	1	NA	intron (NM_207583, intron 1 of 7)	L1Md_T|LINE|L1	20288	NM_207583	240843	Mm.329579	NM_207583	ENSMUSG00000004031	Brinp2	6430517E21Rik|BB361039|Fam5b|mKIAA1747	bone morphogenic protein/retinoic acid inducible neural-specific 2	protein-coding
Merged-chr15-86308069-1	chr15	86307937	86308201	+	1	NA	intron (NM_001358062, intron 4 of 9)	intron (NM_001358062, intron 4 of 9)	30394	NM_001358062	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
Merged-chr15-101230048-1	chr15	101229962	101230134	+	1	NA	intron (NM_019518, intron 4 of 7)	B1_Mur2|SINE|Alu	-4862	NR_045328	380977	Mm.399924	NR_045326	ENSMUSG00000097915	A330009N23Rik	-	RIKEN cDNA A330009N23 gene	ncRNA
Merged-chr7-7495619-1	chr7	7495490	7495748	+	1	NA	Intergenic	Lx2|LINE|L1	-15646	NM_001105063	22311	Mm.482571	NM_001105063	ENSMUSG00000096743	Vmn2r32	V2r5	vomeronasal 2, receptor 32	protein-coding
Merged-chr11-96005277-1	chr11	96005142	96005412	+	1	NA	intron (NM_009951, intron 1 of 14)	CpG	667	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
Merged-chr5-89953466-1	chr5	89953362	89953571	+	1	NA	Intergenic	L1Md_F|LINE|L1	-70132	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
Merged-chr12-82636015-1	chr12	82635900	82636130	+	1	NA	intron (NM_001282061, intron 1 of 16)	L1Md_T|LINE|L1	18516	NM_001282061	50779	Mm.126176	NM_015812	ENSMUSG00000021219	Rgs6	-	regulator of G-protein signaling 6	protein-coding
Merged-chr1-158883371-1	chr1	158883210	158883533	+	1	NA	intron (NM_001085376, intron 2 of 21)	L1Md_T|LINE|L1	74067	NM_001085376	23850	Mm.458621	NM_001085376	ENSMUSG00000073530	Pappa2	PAPP-A2|PLAC3|Pappe	pappalysin 2	protein-coding
Merged-chr15-88965651-1	chr15	88965543	88965759	+	1	NA	intron (NM_133241, intron 7 of 11)	intron (NM_133241, intron 7 of 11)	-11233	NM_172818	239591	Mm.86807	NM_172818	ENSMUSG00000022388	Ttll8	1700019P01Rik|4933401B17	tubulin tyrosine ligase-like family, member 8	protein-coding
Merged-chr19-3669337-1	chr19	3669254	3669420	+	1	NA	intron (NM_008513, intron 1 of 22)	intron (NM_008513, intron 1 of 22)	17227	NM_008513	16973	Mm.274581	NM_008513	ENSMUSG00000024913	Lrp5	BMND1|HBM|LR3|LRP7|OPPG|mKIAA4142	low density lipoprotein receptor-related protein 5	protein-coding
Merged-chr1-141263180-1	chr1	141263097	141263263	+	1	NA	Intergenic	L1Md_A|LINE|L1	-606778	NR_040604	75910	Mm.483845	NR_040604	ENSMUSG00000102368	4930590L20Rik	-	RIKEN cDNA 4930590L20 gene	ncRNA
Merged-chr10-36669163-1	chr10	36669058	36669269	+	1	NA	intron (NM_001081208, intron 2 of 3)	L1Md_T|LINE|L1	162356	NM_001253356	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
Merged-chr11-27823127-1	chr11	27823049	27823206	+	1	NA	Intergenic	L1Md_A|LINE|L1	761197	NM_001346759	216613	Mm.93759	NM_181577	ENSMUSG00000032878	Ccdc85a	-	coiled-coil domain containing 85A	protein-coding
Merged-chr11-36343600-1	chr11	36343496	36343705	+	1	NA	intron (NM_011856, intron 3 of 28)	L1Md_T|LINE|L1	-363511	NM_170779	211652	Mm.31267	NM_170779	ENSMUSG00000018849	Wwc1	AA408228|AU017197|BC037006|Kibra|mKIAA0869	WW, C2 and coiled-coil domain containing 1	protein-coding
Merged-chr15-86294591-1	chr15	86294495	86294687	+	1	NA	intron (NM_001358062, intron 2 of 9)	intron (NM_001358062, intron 2 of 9)	16916	NM_001358062	223754	Mm.28904	NM_145476	ENSMUSG00000051864	Tbc1d22a	BC023106|D15Ertd781e	TBC1 domain family, member 22a	protein-coding
Merged-chr13-68166259-1	chr13	68166154	68166364	+	1	NA	Intergenic	Intergenic	65561	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr1-9179917-1	chr1	9179808	9180027	+	1	NA	intron (NM_027671, intron 2 of 20)	L1Md_A|LINE|L1	119960	NM_001290390	71096	Mm.336395	NM_027671	ENSMUSG00000025909	Sntg1	4933426D16Rik|G1SYN|SYN4	syntrophin, gamma 1	protein-coding
Merged-chr19-30010662-1	chr19	30010569	30010756	+	1	NA	Intergenic	RLTR34D_MM|LTR|ERVK	6872	NM_025741	66745	Mm.158128	NM_025741	ENSMUSG00000024815	Trpd52l3	4931412G03Rik	tumor protein D52-like 3	protein-coding
Merged-chr1-78241773-1	chr1	78241538	78242009	+	1	NA	Intergenic	L1Md_T|LINE|L1	-44637	NM_001159520	18505	Mm.1371	NM_008781	ENSMUSG00000004872	Pax3	Pax-3|Sp|Splchl2|splotch	paired box 3	protein-coding
Merged-chr15-83722666-1	chr15	83722578	83722754	+	1	NA	intron (NM_001271473, intron 1 of 19)	(TC)n|Simple_repeat|Simple_repeat	2373	NM_022723	64706	Mm.40393	NM_022723	ENSMUSG00000016763	Scube1	7330410C13Rik|A630023E24Rik	signal peptide, CUB domain, EGF-like 1	protein-coding
Merged-chr6-140459575-1	chr6	140459477	140459674	+	1	NA	intron (NM_144920, intron 3 of 30)	RLTR13A2|LTR|ERVK	35476	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
Merged-chr10-25937739-1	chr10	25937612	25937866	+	1	NA	Intergenic	L1Md_T|LINE|L1	-100302	NR_045349	73803	Mm.258921	NR_045349	ENSMUSG00000112444	4930401C15Rik	-	RIKEN cDNA 4930401C15 gene	ncRNA
Merged-chr13-60046469-1	chr13	60046381	60046557	+	1	NA	intron (NR_046142, intron 1 of 2)	intron (NR_046142, intron 1 of 2)	16758	NR_046142	328263	Mm.123405	NR_046142	ENSMUSG00000114531	A530065N20Rik	A530065N20	RIKEN cDNA A530046M15 gene	ncRNA
Merged-chr1-44477192-1	chr1	44477102	44477282	+	1	NA	Intergenic	L1Md_T|LINE|L1	-74479	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
Merged-chr17-27384332-1	chr17	27384207	27384457	+	1	NA	Intergenic	Intergenic	26235	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr1-106296254-1	chr1	106296126	106296382	+	1	NA	intron (NM_133821, intron 3 of 16)	L1Md_A|LINE|L1	124385	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
Merged-chr10-22347570-1	chr10	22347491	22347650	+	1	NA	intron (NM_009018, intron 6 of 6)	ETnERV-int|LTR|ERVK	-14324	NM_020030	56554	Mm.458004	NM_020030	ENSMUSG00000078452	Raet1d	RAE-1delta	retinoic acid early transcript delta	protein-coding
Merged-chr1-48230562-1	chr1	48230478	48230646	+	1	NA	Intergenic	L1Md_T|LINE|L1	-763437	NR_105768	102466969		NR_105768	ENSMUSG00000098876	Mir6350	Gm27958|mmu-mir-6350	microRNA 6350	ncRNA
Merged-chr13-55524879-1	chr13	55524790	55524968	+	1	NA	intron (NM_013739, intron 2 of 4)	intron (NM_013739, intron 2 of 4)	3659	NM_013739	27261	Mm.33910	NM_013739	ENSMUSG00000035711	Dok3	AI450713|Dokl	docking protein 3	protein-coding
Merged-chr19-44098818-1	chr19	44098690	44098947	+	1	NA	intron (NM_001162410, intron 4 of 20)	PB1D11|SINE|Alu	8659	NM_007700	12675	Mm.3996	NM_007700	ENSMUSG00000025199	Chuk	AI256658|Chuk1|Fbx24|Fbxo24|IKBKA|IKK alpha|IKK1|Ikka|NFKBIKA	conserved helix-loop-helix ubiquitous kinase	protein-coding
Merged-chr15-89387583-1	chr15	89387502	89387665	+	1	NA	exon (NM_001160178, exon 1 of 1)	exon (NM_001160178, exon 1 of 1)	3524	NM_001160178	546648		NM_001160178	ENSMUSG00000091680	Klhdc7b	EG546648|Gm306	kelch domain containing 7B	protein-coding
Merged-chr12-115294262-1	chr12	115294164	115294360	+	1	NA	Intergenic	Intergenic	401532	NR_105810	102465205		NR_105810	ENSMUSG00000098336	Mir6388	Gm27925|mmu-mir-6388	microRNA 6388	ncRNA
Merged-chr5-102409886-1	chr5	102409667	102410105	+	1	NA	Intergenic	L1Md_T|LINE|L1	-71505	NM_146161	231532	Mm.440191	NM_029270	ENSMUSG00000057315	Arhgap24	0610025G21Rik	Rho GTPase activating protein 24	protein-coding
Merged-chr8-76202398-1	chr8	76202308	76202488	+	1	NA	Intergenic	L1Md_T|LINE|L1	698223	NR_028579	102640923	Mm.367571	NR_028579	ENSMUSG00000074235	Gm10649	-	predicted gene 10649	ncRNA
Merged-chr15-78983161-1	chr15	78983078	78983244	+	1	NA	exon (NM_001024716, exon 1 of 14)	exon (NM_001024716, exon 1 of 14)	105	NM_001024716	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
Merged-chr1-162065716-1	chr1	162065586	162065847	+	1	NA	intron (NM_172646, intron 16 of 19)	L1Md_T|LINE|L1	60747	NR_040562	72753	Mm.452125	NR_040562	ENSMUSG00000090260	2810442N19Rik	-	RIKEN cDNA 2810442N19 gene	ncRNA
Merged-chr1-190615439-1	chr1	190615360	190615519	+	1	NA	Intergenic	L1Md_T|LINE|L1	211791	NR_151624	433390	Mm.331295	NR_151624	ENSMUSG00000103644	Gm29678	-	predicted gene, 29678	ncRNA
Merged-chr17-8718125-1	chr17	8718038	8718212	+	1	NA	intron (NM_001290707, intron 1 of 22)	L1Md_T|LINE|L1	-83620	NM_011866	23984	Mm.87161	NM_011866	ENSMUSG00000023868	Pde10a	-	phosphodiesterase 10A	protein-coding
Merged-chr8-54143570-1	chr8	54143480	54143661	+	1	NA	intron (NM_009506, intron 1 of 6)	IAPEz-int|LTR|ERVK	66038	NM_009506	22341	Mm.1402	NM_009506	ENSMUSG00000031520	Vegfc	AW228853|VEGF-C	vascular endothelial growth factor C	protein-coding
Merged-chr1-131681448-1	chr1	131681354	131681543	+	1	NA	Intergenic	L1Md_T|LINE|L1	-7247	NM_001311096	226421	Mm.44508	NM_145509	ENSMUSG00000052688	Rab7b	5430435G22Rik	RAB7B, member RAS oncogene family	protein-coding
Merged-chr5-60069957-1	chr5	60069874	60070041	+	1	NA	Intergenic	L1Md_T|LINE|L1	-83955	NR_040682	71057	Mm.50817	NR_040682	ENSMUSG00000106013	4933402J10Rik	-	RIKEN cDNA 4933402J10 gene	ncRNA
Merged-chr7-38176281-1	chr7	38176193	38176370	+	1	NA	Intergenic	Intergenic	-6936	NM_001085385	72244	Mm.187554	NM_028166		1600014C10Rik	AI428873	RIKEN cDNA 1600014C10 gene	protein-coding
Merged-chr15-38340861-1	chr15	38340779	38340944	+	1	NA	Intergenic	RodERV21-int|LTR|ERV1	-40150	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
Merged-chr5-89208159-1	chr5	89208075	89208244	+	1	NA	intron (NM_001359211, intron 19 of 26)	MMETn-int|LTR|ERVK	180193	NM_001359213	54403	Mm.41044	NM_018760	ENSMUSG00000060961	Slc4a4	AI835705|NBC|NBC1	solute carrier family 4 (anion exchanger), member 4	protein-coding
Merged-chr1-187068823-1	chr1	187068647	187069000	+	1	NA	intron (NM_028848, intron 9 of 9)	L1Md_T|LINE|L1	55542	NR_151534	105244050		NR_151534		Gm15509	-	predicted gene 15509	ncRNA
Merged-chr1-76314916-1	chr1	76314814	76315018	+	1	NA	Intergenic	L1Md_A|LINE|L1	-174217	NR_038012	620079	Mm.378379	NR_038012	ENSMUSG00000100553	Gm17751	-	predicted gene, 17751	ncRNA
Merged-chr13-55513462-1	chr13	55513284	55513641	+	1	NA	promoter-TSS (NM_026131)	promoter-TSS (NM_026131)	-16	NR_104287	67399	Mm.275648	NM_026131	ENSMUSG00000021493	Pdlim7	LMP	PDZ and LIM domain 7	protein-coding
Merged-chr1-54271532-1	chr1	54271206	54271859	+	1	NA	intron (NM_030025, intron 4 of 27)	L1Md_A|LINE|L1	20849	NM_030025	78016	Mm.67455	NM_030025	ENSMUSG00000025983	Ccdc150	4930511H11Rik	coiled-coil domain containing 150	protein-coding
Merged-chr1-25596324-1	chr1	25596107	25596541	+	1	NA	intron (NM_175642, intron 2 of 30)	L1Md_T|LINE|L1	233383	NM_175642	210933	Mm.336569	NM_175642	ENSMUSG00000033569	Adgrb3	A830096D10Rik|Bai3	adhesion G protein-coupled receptor B3	protein-coding
Merged-chr15-37860670-1	chr15	37860572	37860768	+	1	NA	Intergenic	L1Md_T|LINE|L1	-68242	NM_001359841	52589	Mm.283370	NM_134094	ENSMUSG00000051359	Ncald	AI848120|D030020D09Rik|D15Ertd412e	neurocalcin delta	protein-coding
Merged-chr8-15011175-1	chr8	15011056	15011294	+	1	NA	5' UTR (NM_029116, exon 1 of 2)	5' UTR (NM_029116, exon 1 of 2)	150	NM_029116	74901	Mm.46675	NM_029116	ENSMUSG00000055675	Kbtbd11	2900016B01Rik|4930465M17Rik|mKIAA0711	kelch repeat and BTB (POZ) domain containing 11	protein-coding
Merged-chr13-66726819-1	chr13	66726640	66726998	+	1	NA	Intergenic	RLTR11A2|LTR|ERVK	178531	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr5-105360815-1	chr5	105360700	105360930	+	1	NA	Intergenic	RLTR13A2|LTR|ERVK	-14339	NR_132129	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
Merged-chr1-75712798-1	chr1	75712641	75712955	+	1	NA	Intergenic	L1Md_T|LINE|L1	166336	NM_001357150	20536	Mm.5053	NM_009208	ENSMUSG00000006576	Slc4a3	A930038D23Rik|Ae3	solute carrier family 4 (anion exchanger), member 3	protein-coding
Merged-chr13-67223610-1	chr13	67223530	67223690	+	1	NA	Intergenic	L1MB1|LINE|L1	29104	NM_001048204	218311	Mm.82396	NM_183156	ENSMUSG00000051037	Zfp455	3732412P20Rik|Rslcan-10	zinc finger protein 455	protein-coding
Merged-chr10-57024908-1	chr10	57024790	57025026	+	1	NA	Intergenic	L1Md_T|LINE|L1	461445	NR_045353	74928	Mm.416643	NR_045353	ENSMUSG00000097370	4930467K11Rik	-	RIKEN cDNA 4930467K11 gene	ncRNA
Merged-chr5-146522633-1	chr5	146522539	146522727	+	1	NA	Intergenic	B1_Mur4|SINE|Alu	-3168	NM_001243109	100041554	Mm.460715	NM_001243109	ENSMUSG00000079091	Gm3404	-	predicted gene 3404	protein-coding
Merged-chr15-77658307-1	chr15	77658171	77658444	+	1	NA	Intergenic	RMER17C|LTR|ERVK	-15021	NM_001143686	328563	Mm.17957	NM_001143686	ENSMUSG00000091694	Apol11b	A330102K04Rik	apolipoprotein L 11b	protein-coding
Merged-chr10-122236748-1	chr10	122236620	122236876	+	1	NA	Intergenic	L1Md_T|LINE|L1	117051	NR_027637	100043513	Mm.429141	NR_027637	ENSMUSG00000111952	Gm4489	Gm241	predicted gene 4489	ncRNA
Merged-chr12-23058289-1	chr12	23058127	23058451	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	-48046	NR_015504	69732	Mm.391403	NM_028362	ENSMUSG00000073164	2410018L13Rik	2810480C08Rik	RIKEN cDNA 2410018L13 gene	ncRNA
Merged-chr1-186593474-1	chr1	186593357	186593592	+	1	NA	Intergenic	L1Md_T|LINE|L1	-34793	NR_131124	320449	Mm.404477	NR_131124	ENSMUSG00000103690	A730004F24Rik	-	RIKEN cDNA A730004F24 gene	ncRNA
Merged-chr17-27369442-1	chr17	27369341	27369544	+	1	NA	Intergenic	RMER17A2|LTR|ERVK	11345	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr9-7799258-1	chr9	7799123	7799393	+	1	NA	Intergenic	ERVB7_1-LTR_MM|LTR|ERVK	14868	NR_049191	100885830		NR_049191	ENSMUSG00000093615	Mir5618	Gm23685|mmu-mir-5618	microRNA 5618	ncRNA
Merged-chr15-101272874-1	chr15	101272780	101272969	+	1	NA	exon (NM_010444, exon 5 of 7)	exon (NM_010444, exon 5 of 7)	6028	NM_010444	15370	Mm.119	NM_010444	ENSMUSG00000023034	Nr4a1	GFRP1|Gfrp|Hbr-1|Hbr1|Hmr|N10|NGFI-B|NGFIB|NP10|NUR77-1|NUR77-2|TIS1|TR3|nur77	nuclear receptor subfamily 4, group A, member 1	protein-coding
Merged-chr19-43675431-1	chr19	43675330	43675532	+	1	NA	promoter-TSS (NM_145156)	promoter-TSS (NM_145156)	253	NR_045645	100502982	Mm.313570	NR_045645		BC037704	-	cDNA sequence BC037704	ncRNA
Merged-chr13-68077372-1	chr13	68077214	68077531	+	1	NA	Intergenic	LTRIS_Mus|LTR|ERV1	154448	NR_155296	101056219	Mm.394919	NR_155295		Urml	mach-1	up-regulated in Myc liver	ncRNA
Merged-chr5-38023128-1	chr5	38022987	38023270	+	1	NA	Intergenic	(GGGAGA)n|Simple_repeat|Simple_repeat	-16102	NM_001359398	71116	Mm.18959	NM_026959	ENSMUSG00000029125	Stx18	1810035L21Rik|4933425D03Rik|AU041562	syntaxin 18	protein-coding
Merged-chr12-21071596-1	chr12	21071491	21071701	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-40160	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
Merged-chr8-72134189-1	chr8	72134102	72134276	+	1	NA	Intergenic	Intergenic	-1103	NM_001001491	326618	Mm.295124	NM_001001491	ENSMUSG00000031799	Tpm4	2610528G24Rik|Tpm4.2|Tpm4.2cy	tropomyosin 4	protein-coding
Merged-chr1-109037775-1	chr1	109037587	109037963	+	1	NA	Intergenic	L1Md_T|LINE|L1	-945125	NM_001316743	241201	Mm.213407	NM_172853	ENSMUSG00000026312	Cdh7	9330156F07Rik|CDH7L1	cadherin 7, type 2	protein-coding
Merged-chr15-79828733-1	chr15	79828603	79828864	+	1	NA	exon (NM_028763, exon 5 of 5)	exon (NM_028763, exon 5 of 5)	5600	NM_001013360	504193	Mm.38438	NM_029079	ENSMUSG00000089837	Npcd	Cbx6-Nptxr	neuronal pentraxin chromo domain	protein-coding
Merged-chr16-81029588-1	chr16	81029455	81029721	+	1	NA	Intergenic	L1Md_T|LINE|L1	-171109	NM_001113208	17968	Mm.433941	NM_010954	ENSMUSG00000022762	Ncam2	Ncam-2|Ocam|RNCAM	neural cell adhesion molecule 2	protein-coding
Merged-chr17-14077288-1	chr17	14077203	14077373	+	1	NA	Intergenic	RLTR6-int|LTR|ERV1	126543	NM_172826	240025	Mm.79993	NM_172826	ENSMUSG00000048826	Dact2	2900084M21Rik|A630024E20|Dpr2|Frd2|dapper2	dishevelled-binding antagonist of beta-catenin 2	protein-coding
Merged-chr10-37041191-1	chr10	37041044	37041338	+	1	NA	Intergenic	L1Md_A|LINE|L1	66647	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
Merged-chr17-23332003-1	chr17	23331920	23332086	+	1	NA	Intergenic	IAPEy-int|LTR|ERVK	-11974	NM_001104579	638102	Mm.469849	NM_001104579	ENSMUSG00000091076	Vmn2r115	EG638102|V2Rp4	vomeronasal 2, receptor 115	protein-coding
Merged-chr1-148547201-1	chr1	148547115	148547288	+	1	NA	Intergenic	L1Md_T|LINE|L1	1375238	NM_001305632	18783	Mm.4186	NM_008869	ENSMUSG00000056220	Pla2g4a	Pla2g4|cPLA2|cPLA2-alpha|cPLA2alpha	phospholipase A2, group IVA (cytosolic, calcium-dependent)	protein-coding
Merged-chr9-14584142-1	chr9	14584062	14584223	+	1	NA	intron (NM_001081395, intron 3 of 12)	L1Md_A|LINE|L1	30858	NM_001081395	75723	Mm.159552	NM_001081395	ENSMUSG00000013076	Amotl1	2310010G08Rik|2310067L22Rik|4932416D09Rik|JEAP|mFLJ00155	angiomotin-like 1	protein-coding
Merged-chr10-22299299-1	chr10	22299220	22299378	+	1	NA	intron (NM_009018, intron 6 of 6)	intron (NM_009018, intron 6 of 6)	-7421	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
Merged-chr12-15192030-1	chr12	15191944	15192117	+	1	NA	Intergenic	L1Md_A|LINE|L1	-141641	NR_045960	73972	Mm.107680	NR_045960	ENSMUSG00000113644	4930448C13Rik	-	RIKEN cDNA 4930448C13 gene	ncRNA
Merged-chr10-66488209-1	chr10	66488065	66488354	+	1	NA	Intergenic	L1Md_F2|LINE|L1	342913	NR_131070	77198	Mm.107617	NR_131070	ENSMUSG00000112210	4930407I19Rik	-	RIKEN cDNA 4930407I19 gene	ncRNA
Merged-chr10-63743079-1	chr10	63742994	63743165	+	1	NA	intron (NM_001164376, intron 5 of 17)	L1Md_T|LINE|L1	-77976	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
Merged-chr10-115039282-1	chr10	115039198	115039367	+	1	NA	Intergenic	L1Md_T|LINE|L1	145740	NM_173391	216343	Mm.31597	NM_173391	ENSMUSG00000006764	Tph2	AU043594|Ntph	tryptophan hydroxylase 2	protein-coding
Merged-chr17-22637828-1	chr17	22637711	22637945	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-36570	NM_001362121	100534296	Mm.390939	NM_001362121		Gm9805	-	predicted gene 9805	protein-coding
Merged-chr13-66706630-1	chr13	66706435	66706825	+	1	NA	Intergenic	Intergenic	198720	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr19-19637246-1	chr19	19637151	19637341	+	1	NA	Intergenic	Lx2B|LINE|L1	-526050	NM_001043354	225998	Mm.234641	NM_146095	ENSMUSG00000036192	Rorb	Nr1f2|RZR-beta|RZRB|Rorbeta|hstp	RAR-related orphan receptor beta	protein-coding
Merged-chr15-103301353-1	chr15	103301235	103301472	+	1	NA	Intergenic	Intergenic	9085	NM_030720	80910	Mm.160369	NM_030720	ENSMUSG00000063234	Gpr84	EX33	G protein-coupled receptor 84	protein-coding
Merged-chr7-5836235-1	chr7	5836151	5836319	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	-30790	NM_030742	81017	Mm.160382	NM_030742	ENSMUSG00000058631	Vmn1r63	V1R1|V1rd1|V3R1	vomeronasal 1 receptor 63	protein-coding
Merged-chr19-6428588-1	chr19	6428475	6428702	+	1	NA	exon (NM_001205235, exon 2 of 22)	exon (NM_001205235, exon 2 of 22)	9850	NM_020253	18190	Mm.329616	NM_020253	ENSMUSG00000033768	Nrxn2	6430591O13Rik|mKIAA0921	neurexin II	protein-coding
Merged-chr10-63777191-1	chr10	63777061	63777322	+	1	NA	intron (NM_001164376, intron 5 of 17)	L1Md_A|LINE|L1	-43864	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
Merged-chrX-18505752-1	chrX	18505643	18505861	+	1	NA	Intergenic	L1Md_T|LINE|L1	-44355	NM_175228	75905	Mm.159617	NM_175228	ENSMUSG00000037358	4930578C19Rik	-	RIKEN cDNA 4930578C19 gene	protein-coding
Merged-chr14-16971384-1	chr14	16971261	16971507	+	1	NA	intron (NM_001289760, intron 1 of 9)	LTRIS2|LTR|ERV1	110947	NM_001289761	218772	Mm.259318	NM_011243	ENSMUSG00000017491	Rarb	A830025K23|Hap|Nr1b2	retinoic acid receptor, beta	protein-coding
Merged-chr11-47162174-1	chr11	47162084	47162264	+	1	NA	intron (NM_011891, intron 3 of 7)	L1Md_F2|LINE|L1	217128	NM_011891	24052	Mm.338890	NM_011891	ENSMUSG00000020354	Sgcd	35kDa|delta-SG	sarcoglycan, delta (dystrophin-associated glycoprotein)	protein-coding
Merged-chr1-145471222-1	chr1	145471139	145471306	+	1	NA	Intergenic	L1Md_T|LINE|L1	-695795	NM_022881	64214	Mm.253927	NM_022881	ENSMUSG00000026357	Rgs18	-	regulator of G-protein signaling 18	protein-coding
Merged-chr13-66637634-1	chr13	66637512	66637756	+	1	NA	Intergenic	RLTR48A|LTR|ERV1	-196516	NM_183119	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr19-42409380-1	chr19	42409295	42409466	+	1	NA	intron (NM_001356589, intron 2 of 14)	intron (NM_001356589, intron 2 of 14)	22114	NM_001356588	72832	Mm.313558	NM_145123	ENSMUSG00000042401	Crtac1	2810454P21Rik|AW047536|Crtac1B|Lotus	cartilage acidic protein 1	protein-coding
Merged-chr10-27462549-1	chr10	27462464	27462635	+	1	NA	intron (NM_008481, intron 2 of 63)	L1Md_T|LINE|L1	72683	NR_131034	75855	Mm.402080	NR_131034	ENSMUSG00000101636	4930579H20Rik	-	RIKEN cDNA 4930579H20 gene	ncRNA
Merged-chrX-165646295-1	chrX	165646203	165646387	+	1	NA	Intergenic	MuRRS-int|LTR|ERV1	-318428	NM_001357099	237213	Mm.113877	NM_183427	ENSMUSG00000018589	Glra2	-	glycine receptor, alpha 2 subunit	protein-coding
Merged-chr1-60691245-1	chr1	60691151	60691340	+	1	NA	Intergenic	L1Md_A|LINE|L1	-55143	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
Merged-chr1-114733448-1	chr1	114733256	114733641	+	1	NA	Intergenic	L1Md_A|LINE|L1	-951689	NM_001077425	636808	Mm.101576	NM_001077425	ENSMUSG00000070695	Cntnap5a	Caspr5-1|EG636808	contactin associated protein-like 5A	protein-coding
Merged-chr11-49906208-1	chr11	49906109	49906308	+	1	NA	intron (NM_001347462, intron 1 of 13)	L1Md_T|LINE|L1	4047	NM_001347462	74563	Mm.258798	NM_029004	ENSMUSG00000020374	Rasgef1c	9130006A14Rik	RasGEF domain family, member 1C	protein-coding
Merged-chr15-36308722-1	chr15	36308639	36308805	+	1	NA	Intergenic	Intergenic	-25575	NM_013923	30945	Mm.5181	NM_013923	ENSMUSG00000022280	Rnf19a	AA032313|Dorfin|Rnf19|UIP117|Ubce7ip2|XYbp	ring finger protein 19A	protein-coding
Merged-chr15-99398508-1	chr15	99398423	99398594	+	1	NA	intron (NM_001171036, intron 2 of 10)	RSINE1|SINE|B4	5289	NM_001171035	110213	Mm.16769	NM_026669	ENSMUSG00000023010	Tmbim6	5031406P05Rik|Bi1|Tegt	transmembrane BAX inhibitor motif containing 6	protein-coding
Merged-chr8-20999889-1	chr8	20999643	21000135	+	1	NA	Intergenic	Lx|LINE|L1	-25656	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr10-34924294-1	chr10	34924146	34924442	+	1	NA	Intergenic	L1Md_T|LINE|L1	440894	NM_010237	14302	Mm.332432	NM_010237	ENSMUSG00000019779	Frk	BSK|BSK/IYK|C85044|GTK|RAK	fyn-related kinase	protein-coding
Merged-chr1-134001889-1	chr1	134001748	134002030	+	1	NA	Intergenic	L1Md_T|LINE|L1	-35365	NM_021355	14264	Mm.287146	NM_021355	ENSMUSG00000041559	Fmod	AI131919|AU041740|FM|SLRR2E	fibromodulin	protein-coding
Merged-chr13-65352664-1	chr13	65352581	65352747	+	1	NA	Intergenic	Intergenic	73810	NM_178364	170936	Mm.151546	NM_178364	ENSMUSG00000021514	Zfp369	B930030B22Rik|D230020H11Rik|NRIF2	zinc finger protein 369	protein-coding
Merged-chr13-67995932-1	chr13	67995853	67996012	+	1	NA	Intergenic	IAPEz-int|LTR|ERVK	132606	NM_001001185	408058	Mm.177840	NM_001001185	ENSMUSG00000064063	BC048507	-	cDNA sequence BC048507	protein-coding
Merged-chr19-3323625-1	chr19	3323526	3323725	+	1	NA	intron (NM_013495, intron 1 of 18)	CpG	324	NM_013495	12894	Mm.18522	NM_013495	ENSMUSG00000024900	Cpt1a	C730027G07|CPTI|Cpt1	carnitine palmitoyltransferase 1a, liver	protein-coding
Merged-chr13-62162180-1	chr13	62162074	62162286	+	1	NA	intron (NM_001039239, intron 1 of 3)	L1Md_F2|LINE|L1	32290	NM_001039239	630579	Mm.440905	NM_001039239	ENSMUSG00000074867	Zfp808	EG630579|Gm7036	zinc finger protein 808	protein-coding
Merged-chr5-146499077-1	chr5	146498894	146499261	+	1	NA	Intergenic	MLTR14|LTR|ERV1	-3300	NM_001243114	100041578	Mm.464400	NM_001243114	ENSMUSG00000095557	Gm3415	-	predicted gene 3415	protein-coding
Merged-chr15-36434882-1	chr15	36434762	36435002	+	1	NA	Intergenic	Intergenic	61852	NM_001358007	68839	Mm.396537	NM_175134	ENSMUSG00000048307	Ankrd46	1110054N06Rik|AI314978|AI987733	ankyrin repeat domain 46	protein-coding
Merged-chr13-44714158-1	chr13	44714065	44714252	+	1	NA	Intergenic	MTA_Mm|LTR|ERVL-MaLR	-16616	NM_001205044	16468	Mm.25059	NM_021878	ENSMUSG00000038518	Jarid2	Jmj|jumonji	jumonji, AT rich interactive domain 2	protein-coding
Merged-chr8-11555712-1	chr8	11555596	11555829	+	1	NA	promoter-TSS (NM_011919)	promoter-TSS (NM_011919)	-50	NM_001302458	26356	Mm.25709	NM_011919	ENSMUSG00000045969	Ing1	2610028J21Rik|AA407184|AI875420|mING1h|p33Ing1|p37Ing1b	inhibitor of growth family, member 1	protein-coding
Merged-chr10-22332215-1	chr10	22332014	22332416	+	1	NA	intron (NM_009018, intron 6 of 6)	L1_Mus1|LINE|L1	25495	NR_015465	606736	Mm.387042	NR_015465	ENSMUSG00000097352	C920009B18Rik	-	RIKEN cDNA C920009B18 gene	ncRNA
Merged-chr1-119747421-1	chr1	119747236	119747606	+	1	NA	intron (NM_019933, intron 8 of 26)	L1Md_T|LINE|L1	89650	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
Merged-chr17-36048245-1	chr17	36048137	36048354	+	1	NA	intron (NM_001034909, intron 1 of 2)	intron (NM_001034909, intron 1 of 2)	5284	NM_001034909	547347	Mm.484641	NM_001034909	ENSMUSG00000073407	Gm6034	EG547347|H2-gs14-2	predicted gene 6034	protein-coding
Merged-chr11-13620034-1	chr11	13619864	13620204	+	1	NA	Intergenic	L1Md_T|LINE|L1	559007	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr12-68439634-1	chr12	68439551	68439717	+	1	NA	Intergenic	L1Md_T|LINE|L1	719552	NM_009093	20090	Mm.379006	NM_009093	ENSMUSG00000034892	Rps29	-	ribosomal protein S29	protein-coding
Merged-chr10-43511573-1	chr10	43511482	43511665	+	1	NA	exon (NM_199028, exon 4 of 4)	exon (NM_199028, exon 4 of 4)	18408	NM_001359600	331623	Mm.490388	NM_199028	ENSMUSG00000038214	Bend3	mKIAA1553	BEN domain containing 3	protein-coding
Merged-chr17-36216360-1	chr17	36216227	36216493	+	1	NA	Intergenic	Intergenic	-26209	NM_008208	15043	Mm.426002	NM_008208	ENSMUSG00000054128	H2-T3	H-2T3|H2-Tw3|MumuTL|TL	histocompatibility 2, T region locus 3	protein-coding
Merged-chr14-51591470-1	chr14	51591347	51591594	+	1	NA	intron (NM_001013816, intron 1 of 4)	intron (NM_001013816, intron 1 of 4)	38680	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr1-146007739-1	chr1	146007557	146007922	+	1	NA	Intergenic	L1Md_T|LINE|L1	-487890	NM_001357571	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr13-66824846-1	chr13	66824654	66825039	+	1	NA	Intergenic	Intergenic	80504	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr15-85646403-1	chr15	85646271	85646536	+	1	NA	Intergenic	Intergenic	-57370	NR_110483	102800312	Mm.33117	NR_110483		Lncppara	Lincppara|Mirlet7bhg|linc-Ppara	long noncoding RNA near Ppara	ncRNA
Merged-chr15-76667098-1	chr15	76667000	76667197	+	1	NA	exon (NM_001358912, exon 17 of 18)	exon (NM_001358912, exon 17 of 18)	2850	NM_007989	14106	Mm.42011	NM_007989	ENSMUSG00000033837	Foxh1	Fast1|Fast2|fast-1|fast-2	forkhead box H1	protein-coding
Merged-chr17-38562687-1	chr17	38562547	38562827	+	1	NA	Intergenic	B2_Mm2|SINE|B2	8495	NM_001177585	100126773	Mm.471587	NM_001177585	ENSMUSG00000092244	Esp34	Gm20410	exocrine gland secreted peptide 34	protein-coding
Merged-chr11-49367227-1	chr11	49367075	49367379	+	1	NA	Intergenic	L1Md_T|LINE|L1	26693	NM_147065	259068	Mm.377819	NM_147065	ENSMUSG00000045421	Olfr1390	MOR256-2	olfactory receptor 1390	protein-coding
Merged-chr15-76252451-1	chr15	76252260	76252642	+	1	NA	Intergenic	MER90a|LTR|ERV1	4260	NR_105918	102465575		NR_105918	ENSMUSG00000098625	Mir6953	Gm27738|mmu-mir-6953	microRNA 6953	ncRNA
Merged-chr1-143086891-1	chr1	143086810	143086972	+	1	NA	Intergenic	L1_Mur3|LINE|L1	-553806	NM_020025	26878	Mm.285580	NM_020025	ENSMUSG00000033849	B3galt2	-	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 2	protein-coding
Merged-chr17-27402096-1	chr17	27401969	27402224	+	1	NA	Intergenic	LTR16E1|LTR|ERVL	43999	NR_106077	102466228		NR_106077	ENSMUSG00000106215	Mir7218	mmu-mir-7218	microRNA 7218	ncRNA
Merged-chr15-77820118-1	chr15	77820039	77820197	+	1	NA	intron (NM_022410, intron 1 of 40)	intron (NM_022410, intron 1 of 40)	22057	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
Merged-chr5-21241273-1	chr5	21241114	21241433	+	1	NA	intron (NR_153365, intron 11 of 26)	IAPEz-int|LTR|ERVK	55006	NM_001359877	212167	Mm.121705	NM_175437	ENSMUSG00000039934	Gsap	A530088I07Rik|Pion	gamma-secretase activating protein	protein-coding
Merged-chr1-146671902-1	chr1	146671755	146672050	+	1	NA	intron (NM_001357572, intron 3 of 8)	L1Md_T|LINE|L1	174215	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr13-62503660-1	chr13	62503574	62503746	+	1	NA	Intergenic	Intergenic	-36848	NM_178875	71508	Mm.442497	NM_178875	ENSMUSG00000113450	Zfp935	8430426H19Rik|Es113	zinc finger protein 935	protein-coding
Merged-chr1-61497132-1	chr1	61497043	61497221	+	1	NA	Intergenic	L1Md_T|LINE|L1	118700	NR_040483	77341	Mm.402964	NR_040483	ENSMUSG00000085447	9530026F06Rik	-	RIKEN cDNA 9530026F06 gene	ncRNA
Merged-chr19-16952104-1	chr19	16952015	16952194	+	1	NA	Intergenic	RMER17B2|LTR|ERVK	-4014	NM_181348	353211	Mm.257354	NM_181348	ENSMUSG00000039126	Prune2	6330414G02Rik|A230083H22Rik|A330102H22Rik|Bmcc1|mKIAA0367	prune homolog 2	protein-coding
Merged-chr15-78955119-1	chr15	78954994	78955244	+	1	NA	intron (NM_001039156, intron 3 of 24)	intron (NM_001039156, intron 3 of 24)	7395	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
Merged-chr13-66433476-1	chr13	66433165	66433788	+	1	NA	exon (NM_183119, exon 3 of 5)	exon (NM_183119, exon 3 of 5)	7642	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr17-30607776-1	chr17	30607655	30607897	+	1	NA	intron (NM_001113560, intron 1 of 6)	B4|SINE|B4	4883	NM_001113560	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
Merged-chr1-27144732-1	chr1	27144635	27144830	+	1	NA	Intergenic	L1Md_T|LINE|L1	-457272	NM_001033764	210940	Mm.297614	NM_001033764	ENSMUSG00000073722	4931408C20Rik	-	RIKEN cDNA 4931408C20 gene	protein-coding
Merged-chr19-7631354-1	chr19	7631253	7631456	+	1	NA	intron (NM_025731, intron 4 of 5)	L1Md_F2|LINE|L1	18785	NM_025731	66727	Mm.116803	NM_025731	ENSMUSG00000024973	Hrasls5	1700055A14Rik|1700086E08Rik|4921526K24Rik|HRSL5|iNAT	HRAS-like suppressor family, member 5	protein-coding
Merged-chr15-51796979-1	chr15	51796897	51797061	+	1	NA	intron (NM_080635, intron 4 of 7)	intron (NM_080635, intron 4 of 7)	68482	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
Merged-chr19-46502301-1	chr19	46502212	46502390	+	1	NA	5' UTR (NM_053100, exon 1 of 6)	5' UTR (NM_053100, exon 1 of 6)	653	NM_053100	93679	Mm.392177	NM_053100	ENSMUSG00000025034	Trim8	AA408830|BB006755|GERP|Rnf27	tripartite motif-containing 8	protein-coding
Merged-chr1-148071162-1	chr1	148070994	148071331	+	1	NA	Intergenic	L1Md_T|LINE|L1	1573475	NM_001357572	215378	Mm.441817	NM_153539	ENSMUSG00000035131	Brinp3	B830045N13Rik|Fam5c	bone morphogenetic protein/retinoic acid inducible neural specific 3	protein-coding
Merged-chr17-17223649-1	chr17	17223448	17223850	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-11254	NM_001362181	102640673		NM_001362181		LOC102640673	-	zinc finger protein 431-like	protein-coding
Merged-chr3-158634892-1	chr3	158634807	158634977	+	1	NA	Intergenic	IAPLTR1a_Mm|LTR|ERVK	-72671	NM_001291452	242274	Mm.132162	NM_001081358	ENSMUSG00000028176	Lrrc7	AK122498|densin|mKIAA1365	leucine rich repeat containing 7	protein-coding
Merged-chr13-66388937-1	chr13	66388816	66389059	+	1	NA	Intergenic	B1_Mus1|SINE|Alu	52181	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr7-58883227-1	chr7	58883114	58883341	+	1	NA	Intergenic	L1Md_A|LINE|L1	225025	NM_009728	11982	Mm.135129	NM_009728	ENSMUSG00000025324	Atp10a	Atp10c|pfatp	ATPase, class V, type 10A	protein-coding
Merged-chr15-66658436-1	chr15	66658323	66658549	+	1	NA	Intergenic	L1Md_F2|LINE|L1	-12334	NM_009375	21819	Mm.441333	NM_009375	ENSMUSG00000053469	Tg	Tgn|cog	thyroglobulin	protein-coding
Merged-chr17-29367096-1	chr17	29367016	29367177	+	1	NA	exon (NM_013710, exon 5 of 16)	exon (NM_013710, exon 5 of 16)	6182	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
Merged-chr10-80020063-1	chr10	80019964	80020163	+	1	NA	intron (NM_027521, intron 1 of 21)	intron (NM_027521, intron 1 of 21)	388	NM_027521	70719	Mm.243954	NM_027521	ENSMUSG00000035697	Arhgap45	6330406L22Rik|AW539505|Ha-1|Hmha1	Rho GTPase activating protein 45	protein-coding
Merged-chr4-108284341-1	chr4	108284260	108284423	+	1	NA	intron (NM_001033634, intron 1 of 13)	IAPLTR1a_Mm|LTR|ERVK	16749	NM_001033634	414872	Mm.426241	NM_001033634	ENSMUSG00000034636	Zyg11b	1110046I03Rik|2810482G21Rik|D4Mgi23|Gm431|mKIAA1730	zyg-ll family member B, cell cycle regulator	protein-coding
Merged-chr10-116172557-1	chr10	116172419	116172695	+	1	NA	intron (NM_001358484, intron 3 of 12)	L1Md_T|LINE|L1	-4701	NM_001161839	19279	Mm.336316	NM_011217	ENSMUSG00000020151	Ptprr	Gmcp1|PTP-SL|PTPBR7|RPTPRR|mPTP213	protein tyrosine phosphatase, receptor type, R	protein-coding
Merged-chr1-166873285-1	chr1	166873153	166873418	+	1	NA	Intergenic	L1Md_T|LINE|L1	126445	NR_037988	100503962	Mm.216842	NR_037988	ENSMUSG00000102548	Gm16701	-	predicted gene, 16701	ncRNA
Merged-chr13-66295132-1	chr13	66294993	66295271	+	1	NA	Intergenic	RLTR33|LTR|ERVK	145986	NM_001290196	76803	Mm.183391	NM_183119	ENSMUSG00000074832	2410141K09Rik	4930482J15Rik|Ayu21-35|Gt(pU21)35Imeg	RIKEN cDNA 2410141K09 gene	protein-coding
Merged-chr13-66707360-1	chr13	66707220	66707500	+	1	NA	Intergenic	Intergenic	197990	NM_026219	67530	Mm.379136	NM_026219	ENSMUSG00000021520	Uqcrb	2210415M14Rik|QP-C|QPC|UQBC|UQBP|UQPC	ubiquinol-cytochrome c reductase binding protein	protein-coding
Merged-chr19-4133347-1	chr19	4133257	4133437	+	1	NA	Intergenic	B4A|SINE|B4	6262	NM_144532	73660	Mm.379226	NM_144532	ENSMUSG00000024842	Cabp4	2410038D05Rik	calcium binding protein 4	protein-coding
Merged-chr2-38902473-1	chr2	38902370	38902577	+	1	NA	intron (NM_010264, intron 1 of 10)	L1Md_F2|LINE|L1	23988	NM_010264	14536	Mm.439703	NM_010264	ENSMUSG00000063972	Nr6a1	1700113M01Rik|Gcnf|NCNF|RTR	nuclear receptor subfamily 6, group A, member 1	protein-coding
Merged-chr19-6234656-1	chr19	6234559	6234753	+	1	NA	exon (NM_198168, exon 2 of 14)	exon (NM_198168, exon 2 of 14)	1184	NM_198168	225849	Mm.118076	NM_198168	ENSMUSG00000024777	Ppp2r5b	B'beta|BC026670	protein phosphatase 2, regulatory subunit B', beta	protein-coding
Merged-chr7-10021198-1	chr7	10021101	10021295	+	1	NA	Intergenic	RMER10A|LTR|ERVL	-29059	NM_001105156	625605	Mm.484763	NM_001105156	ENSMUSG00000096180	Vmn2r49	-	vomeronasal 2, receptor 49	protein-coding
Merged-chr12-13992868-1	chr12	13992779	13992958	+	1	NA	Intergenic	L1Md_T|LINE|L1	159170	NM_029007	105005	Mm.227253	NM_029007	ENSMUSG00000020607	Fam84a	2310003N02Rik|4731402F03Rik|AW125753|Nse1	family with sequence similarity 84, member A	protein-coding
Merged-chr11-98775413-1	chr11	98775331	98775495	+	1	NA	promoter-TSS (NM_145434)	promoter-TSS (NM_145434)	-36	NM_145434	217166	Mm.390397	NM_145434	ENSMUSG00000020889	Nr1d1	A530070C09Rik|R75201	nuclear receptor subfamily 1, group D, member 1	protein-coding
Merged-chr1-36954491-1	chr1	36954322	36954661	+	1	NA	Intergenic	L1Md_T|LINE|L1	-14964	NM_018872	56030	Mm.186943	NM_018872	ENSMUSG00000026116	Tmem131	2610524E03Rik|CC28|D1Bwg0491e|Neg|RW1|YR-23|mKIAA0257	transmembrane protein 131	protein-coding
Merged-chr10-6656245-1	chr10	6656163	6656328	+	1	NA	Intergenic	L1Md_A|LINE|L1	-102348	NM_001302796	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
Merged-chr1-95235112-1	chr1	95235009	95235215	+	1	NA	Intergenic	L1Md_A|LINE|L1	-78516	NM_026321	67698	Mm.272705	NM_026321	ENSMUSG00000051185	Fam174a	2310044D20Rik|Fam174|Naa6|Tmem157	family with sequence similarity 174, member A	protein-coding
Merged-chr10-63667019-1	chr10	63666815	63667223	+	1	NA	intron (NM_001164376, intron 5 of 17)	L1Md_A|LINE|L1	-154036	NM_001164519	216033	Mm.444692	NM_177612	ENSMUSG00000060843	Ctnna3	4930429L08Rik|4933408A16|Catna3|Vr22	catenin (cadherin associated protein), alpha 3	protein-coding
Merged-chr17-65084250-1	chr17	65084111	65084390	+	1	NA	Intergenic	RLTR10-int|LTR|ERVK	-248179	NM_030031	78057	Mm.109380	NM_030031	ENSMUSG00000024088	4930583I09Rik	-	RIKEN cDNA 4930583I09 gene	protein-coding
Merged-chr11-10704276-1	chr11	10704136	10704417	+	1	NA	Intergenic	L1Md_T|LINE|L1	-409740	NM_177033	319922	Mm.337851	NM_177033	ENSMUSG00000050830	Vwc2	A930041G11Rik|G11|PSST739|UNQ739|cradin	von Willebrand factor C domain containing 2	protein-coding
Merged-chr10-4916061-1	chr10	4915953	4916170	+	1	NA	intron (NM_001302531, intron 5 of 8)	L1Md_T|LINE|L1	153002	NM_022027	64009	Mm.331626	NM_022027	ENSMUSG00000096054	Syne1	8B|A330049M09Rik|BE692247|C130039F11Rik|CPG2|KASH1|Myne1|mKIAA1756|myne-1	spectrin repeat containing, nuclear envelope 1	protein-coding
Merged-chr13-50296490-1	chr13	50296359	50296621	+	1	NA	Intergenic	L1Md_T|LINE|L1	34675	NR_045474	69211	Mm.259768	NR_045474		2310081J21Rik	-	RIKEN cDNA 2310081J21 gene	ncRNA
Merged-chr19-3830194-1	chr19	3830112	3830276	+	1	NA	Intergenic	RMER15|LTR|ERVL	-21579	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
Merged-chr15-74733295-1	chr15	74733214	74733377	+	1	NA	intron (NM_026671, intron 1 of 2)	intron (NM_026671, intron 1 of 2)	1018	NM_026671	68311	Mm.306880	NM_026671	ENSMUSG00000022595	Lypd2	0610005K03Rik|Lypdc2|VLL	Ly6/Plaur domain containing 2	protein-coding
Merged-chr11-51019475-1	chr11	51019307	51019643	+	1	NA	Intergenic	L1Md_A|LINE|L1	-7529	NM_010997	18354	Mm.222843	NM_010997	ENSMUSG00000059397	Olfr54	F3|MOR126-1	olfactory receptor 54	protein-coding
Merged-chr19-9419735-1	chr19	9419648	9419822	+	1	NA	Intergenic	ORR1A2-int|LTR|ERVL-MaLR	139513	NR_073559	619371	Mm.316894	NM_001030317		Stxbp3-ps	Munc18c(L)|Stxbp3-1|Stxbp3b	syntaxin-binding protein 3, pseudogene	pseudo
Merged-chr11-75668716-1	chr11	75668225	75669207	+	1	NA	intron (NM_001080774, intron 19 of 31)	intron (NM_001080774, intron 19 of 31)	-10543	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
Merged-chr1-101761595-1	chr1	101761479	101761711	+	1	NA	Intergenic	L1Md_T|LINE|L1	605827	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr19-5207113-1	chr19	5207034	5207193	+	1	NA	intron (NM_153129, intron 1 of 23)	intron (NM_153129, intron 1 of 23)	66006	NM_153129	107975	Mm.234923	NM_153129	ENSMUSG00000024855	Pacs1	AI325977	phosphofurin acidic cluster sorting protein 1	protein-coding
Merged-chr1-70876044-1	chr1	70875912	70876177	+	1	NA	intron (NM_177164, intron 3 of 3)	L1Md_A|LINE|L1	150329	NM_001310658	320460	Mm.360649	NM_177164	ENSMUSG00000045648	Vwc2l	A830006F12Rik|Brl	von Willebrand factor C domain-containing protein 2-like	protein-coding
Merged-chr10-86237607-1	chr10	86237514	86237701	+	1	NA	intron (NM_013722, intron 6 of 13)	L1Md_T|LINE|L1	-62805	NM_011595	21859	Mm.4871	NM_011595	ENSMUSG00000020044	Timp3	Timp-3	tissue inhibitor of metalloproteinase 3	protein-coding
Merged-chr6-23480411-1	chr6	23480300	23480523	+	1	NA	intron (NM_153163, intron 8 of 29)	L1Md_A|LINE|L1	169894	NM_198251	386611	Mm.436547	NM_198251	ENSMUSG00000051956	Rnf133	Greul2	ring finger protein 133	protein-coding
Merged-chr5-146509955-1	chr5	146509789	146510121	+	1	NA	intron (NM_001243114, intron 2 of 4)	B3|SINE|B2	-4168	NM_001243111	100041548	Mm.489581	NM_001243111	ENSMUSG00000041505	Gm3402	-	predicted gene 3402	protein-coding
Merged-chr15-78953740-1	chr15	78953661	78953820	+	1	NA	intron (NM_001039156, intron 3 of 24)	intron (NM_001039156, intron 3 of 24)	6016	NM_001039155	110253	Mm.123714	NM_138579	ENSMUSG00000033088	Triobp	AI428493|EST478828|Tara|mKIAA1662	TRIO and F-actin binding protein	protein-coding
Merged-chr1-4562211-1	chr1	4562049	4562373	+	1	NA	Intergenic	L1Md_T|LINE|L1	-64857	NM_011441	20671	Mm.279103	NM_011441	ENSMUSG00000025902	Sox17	-	SRY (sex determining region Y)-box 17	protein-coding
Merged-chr14-51617280-1	chr14	51617198	51617363	+	1	NA	intron (NM_001013816, intron 1 of 4)	L1_Mus3|LINE|L1	64490	NM_001013816	434459	Mm.359230	NM_001013816	ENSMUSG00000079244	Gm5622	EG434459	predicted gene 5622	protein-coding
Merged-chr10-15339799-1	chr10	15339648	15339951	+	1	NA	Intergenic	L1Md_A|LINE|L1	-451978	NR_131087	77538	Mm.128235	NR_131087	ENSMUSG00000112227	C330004P14Rik	-	RIKEN cDNA C330004P14 gene	ncRNA
Merged-chr11-13617464-1	chr11	13617383	13617546	+	1	NA	Intergenic	L1Md_T|LINE|L1	561577	NR_131011	75280	Mm.108492	NR_131011	ENSMUSG00000085452	4930554G24Rik	-	RIKEN cDNA 4930554G24 gene	ncRNA
Merged-chr19-29102112-1	chr19	29101967	29102257	+	1	NA	intron (NM_021525, intron 1 of 8)	AT_rich|Low_complexity|Low_complexity	737	NM_021525	59028	Mm.28630	NM_021525	ENSMUSG00000024785	Rcl1	2310040A02Rik|AI789745|C76567|RPCL1|Rnac	RNA terminal phosphate cyclase-like 1	protein-coding
Merged-chr11-89962959-1	chr11	89962844	89963074	+	1	NA	Intergenic	L1Md_T|LINE|L1	39935	NM_001316372	18559	Mm.5062	NM_008796	ENSMUSG00000020553	Pctp	PC-TP|StarD2	phosphatidylcholine transfer protein	protein-coding
Merged-chr2-12043414-1	chr2	12043316	12043512	+	1	NA	Intergenic	IAPLTR2_Mm|LTR|ERVK	-257832	NR_040353	338535	Mm.483275	NR_040353	ENSMUSG00000086843	E030013I19Rik	-	RIKEN cDNA E030013I19 gene	ncRNA
Merged-chr15-83616690-1	chr15	83616592	83616788	+	1	NA	exon (NM_001271472, exon 16 of 23)	exon (NM_001271472, exon 16 of 23)	-21533	NM_183017	223723	Mm.46778	NM_183017	ENSMUSG00000016757	Ttll12	BC055368|D430005B17	tubulin tyrosine ligase-like family, member 12	protein-coding
Merged-chr16-92145219-1	chr16	92145099	92145340	+	1	NA	Intergenic	MTA_Mm-int|LTR|ERVL-MaLR	86883	NM_080456	121022	Mm.217354	NM_080456	ENSMUSG00000039680	Mrps6	AW046321	mitochondrial ribosomal protein S6	protein-coding
Merged-chr1-165407864-1	chr1	165407762	165407966	+	1	NA	intron (NM_028759, intron 6 of 18)	L1Md_Gf|LINE|L1	52599	NM_028759	74106	Mm.227605	NM_028759	ENSMUSG00000026571	Dcaf6	1200006M05Rik|Iqwd1|PC326	DDB1 and CUL4 associated factor 6	protein-coding
Merged-chr5-145631644-1	chr5	145631517	145631772	+	1	NA	Intergenic	Intergenic	-46914	NM_001105159	100041375	Mm.489591	NM_001105159	ENSMUSG00000075552	Cyp3a41b	-	cytochrome P450, family 3, subfamily a, polypeptide 41B	protein-coding
Merged-chr5-105366886-1	chr5	105366709	105367063	+	1	NA	Intergenic	RLTR13A2|LTR|ERVK	-20410	NR_132129	634650	Mm.458435	NM_001039647	ENSMUSG00000092021	Gbp11	EG634650|Gm7141	guanylate binding protein 11	protein-coding
Merged-chr10-19980632-1	chr10	19980538	19980726	+	1	NA	intron (NM_008580, intron 1 of 29)	L1Md_T|LINE|L1	46106	NM_008580	26408	Mm.6595	NM_008580	ENSMUSG00000071369	Map3k5	7420452D20Rik|ASK|ASK1|MAPKKK5|Mekk5	mitogen-activated protein kinase kinase kinase 5	protein-coding
Merged-chr15-102625552-1	chr15	102625439	102625665	+	1	NA	promoter-TSS (NM_001310070)	promoter-TSS (NM_001310070)	-88	NM_001310067	223922	Mm.208714	NM_146065	ENSMUSG00000099083	Atf7	1110012F10Rik|9430065F09Rik|AI549878|C130020M04Rik	activating transcription factor 7	protein-coding
Merged-chr1-60692297-1	chr1	60692177	60692418	+	1	NA	Intergenic	L1Md_A|LINE|L1	-54091	NM_007642	12487	Mm.255003	NM_007642	ENSMUSG00000026012	Cd28	-	CD28 antigen	protein-coding
Merged-chr1-32081862-1	chr1	32081778	32081946	+	1	NA	Intergenic	L1Md_A|LINE|L1	-90860	NM_133235	170771	Mm.336594	NM_133235	ENSMUSG00000026058	Khdrbs2	6330586C16Rik|Slim1|Slm-1|Slm1|TG-RP135|Tg(LRRK2*R1441G)135Cjli|mSLM-1	KH domain containing, RNA binding, signal transduction associated 2	protein-coding
Merged-chr11-98944868-1	chr11	98944787	98944949	+	1	NA	intron (NM_001177303, intron 1 of 8)	intron (NM_001177303, intron 1 of 8)	5157	NM_001177303	19401	Mm.439744	NM_009024	ENSMUSG00000037992	Rara	Nr1b1|RAR|RARalpha1	retinoic acid receptor, alpha	protein-coding
Merged-chr16-97091370-1	chr16	97091283	97091457	+	1	NA	intron (NM_031174, intron 1 of 32)	L1Md_T|LINE|L1	79365	NM_031174	13508	Mm.102437	NM_031174	ENSMUSG00000050272	Dscam	4932410A21Rik	DS cell adhesion molecule	protein-coding
Merged-chr1-139913059-1	chr1	139912943	139913176	+	1	NA	Intergenic	L1Md_T|LINE|L1	-54360	NM_001025575	545366	Mm.439660	NM_001025575	ENSMUSG00000033898	Cfhr2	Cfhrb_4/2	complement factor H-related 2	protein-coding
Merged-chr1-30377623-1	chr1	30377507	30377740	+	1	NA	Intergenic	L1Md_A|LINE|L1	485633	NM_001081080	213109	Mm.194486	NM_025871	ENSMUSG00000048874	Phf3	2310061N19Rik	PHD finger protein 3	protein-coding
Merged-chr19-5739500-1	chr19	5739400	5739601	+	1	NA	Intergenic	Intergenic	-1404	NM_008520	16998	Mm.182396	NM_008520	ENSMUSG00000024940	Ltbp3	Ltbp2|mFLJ00070	latent transforming growth factor beta binding protein 3	protein-coding
Merged-chr1-103292933-1	chr1	103292825	103293042	+	1	NA	Intergenic	L1Md_T|LINE|L1	-1475587	NM_011800	23836	Mm.103640	NM_011800	ENSMUSG00000050840	Cdh20	Cdh7	cadherin 20	protein-coding
Merged-chr8-84832626-1	chr8	84832539	84832714	+	1	NA	promoter-TSS (NR_033145)	promoter-TSS (NR_033145)	344	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
Merged-chr8-20992569-1	chr8	20992458	20992681	+	1	NA	Intergenic	Intergenic	-32976	NM_183253	66298	Mm.482941	NM_183253	ENSMUSG00000074447	Defa21	2010016B13Rik|Defcr21	defensin, alpha, 21	protein-coding
Merged-chr15-73510302-1	chr15	73510208	73510396	+	1	NA	Intergenic	B1_Mur1|SINE|Alu	-2258	NR_152151	105841	Mm.322557	NM_001081066	ENSMUSG00000036661	Dennd3	AI447457|E030003N15Rik	DENN/MADD domain containing 3	protein-coding
Merged-chr1-20279300-1	chr1	20279137	20279463	+	1	NA	intron (NM_153179, intron 51 of 66)	L1Md_T|LINE|L1	-77154	NR_045734	75028	Mm.417820	NR_045734	ENSMUSG00000089914	4930486I03Rik	-	RIKEN cDNA 4930486I03 gene	ncRNA
Merged-chr10-36822478-1	chr10	36822370	36822587	+	1	NA	intron (NM_001253355, intron 4 of 5)	L1Md_T|LINE|L1	-152066	NM_008229	15182	Mm.19806	NM_008229	ENSMUSG00000019777	Hdac2	D10Wsu179e|YAF1|Yy1bp|mRPD3	histone deacetylase 2	protein-coding
Merged-chr1-158643629-1	chr1	158643416	158643842	+	1	NA	intron (NM_007495, intron 16 of 22)	L1Md_T|LINE|L1	138004	NR_030441	735253		NR_030441	ENSMUSG00000070103	Mir488	Mirn488|mir-488|mmu-mir-488	microRNA 488	ncRNA
Merged-chr11-17033345-1	chr11	17033234	17033456	+	1	NA	Intergenic	L1Md_A|LINE|L1	-18589	NM_029861	380686	Mm.425666	NM_029861	ENSMUSG00000044629	Cnrip1	1500041B16Rik|3110054C06Rik|5330437A18Rik|AI854501|C2orf32	cannabinoid receptor interacting protein 1	protein-coding
Merged-chr11-42782248-1	chr11	42782164	42782332	+	1	NA	Intergenic	L1Md_T|LINE|L1	360898	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
Merged-chr1-118763682-1	chr1	118763567	118763798	+	1	NA	Intergenic	L1Md_T|LINE|L1	135737	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
Merged-chr13-34103215-1	chr13	34103038	34103392	+	1	NA	intron (NR_046184, intron 2 of 4)	intron (NR_046184, intron 2 of 4)	10057	NR_046184	432745	Mm.159104	NR_046184	ENSMUSG00000113591	4930447K03Rik	-	RIKEN cDNA 4930447K03 gene	ncRNA
Merged-chr15-103762302-1	chr15	103762058	103762546	+	1	NA	intron (NM_009268, intron 2 of 5)	RMER1C|Other|Other	-6804	NR_126081	20771	Mm.30276	NM_009268	ENSMUSG00000060311	Mucl1	Spt-2|Spt2	mucin-like 1	protein-coding
Merged-chr19-42570746-1	chr19	42570667	42570826	+	1	NA	intron (NM_177464, intron 2 of 6)	intron (NM_177464, intron 2 of 6)	42060	NM_053083	67573	Mm.178767	NM_053083	ENSMUSG00000025185	Loxl4	4833426I20Rik|Loxc	lysyl oxidase-like 4	protein-coding
Merged-chr15-76540742-1	chr15	76540635	76540850	+	1	NA	exon (NM_029643, exon 4 of 5)	exon (NM_029643, exon 4 of 5)	1799	NM_029643	52710	Mm.28597	NM_029643	ENSMUSG00000022560	Slc52a2	2010003P03Rik|D15Ertd747e|GPCR42|Gpr172b|PAR2|mRFT1	solute carrier protein 52, member 2	protein-coding
Merged-chr1-101306027-1	chr1	101305932	101306122	+	1	NA	Intergenic	L1Md_T|LINE|L1	150259	NR_037989	100504525	Mm.87065	NR_037989	ENSMUSG00000100684	Gm20268	-	predicted gene, 20268	ncRNA
Merged-chr1-42338380-1	chr1	42338137	42338623	+	1	NA	Intergenic	L1Md_T|LINE|L1	356445	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
Merged-chr10-47802090-1	chr10	47801927	47802254	+	1	NA	Intergenic	L1Md_T|LINE|L1	1557341	NR_028276	108637		NR_028276	ENSMUSG00000096263	Snord14c	Gm23107|Rnu14|U14	small nucleolar RNA, C/D box 14C	snoRNA
Merged-chr10-36422213-1	chr10	36422099	36422328	+	1	NA	Intergenic	L1Md_A|LINE|L1	-84594	NM_001253355	319415	Mm.332442	NM_001081208	ENSMUSG00000044499	Hs3st5	D930005L05Rik|Gm1151|Hs3ost5	heparan sulfate (glucosamine) 3-O-sulfotransferase 5	protein-coding
Merged-chr2-156574792-1	chr2	156574713	156574871	+	1	NA	Intergenic	Intergenic	27216	NM_001164818	68295	Mm.253648	NM_026661	ENSMUSG00000027628	Aar2	0610011L14Rik	AAR2 splicing factor homolog	protein-coding
Merged-chr8-62161189-1	chr8	62161047	62161332	+	1	NA	Intergenic	L1Md_T|LINE|L1	-37996	NM_011922	26359	Mm.42179	NM_011922	ENSMUSG00000031635	Anxa10	-	annexin A10	protein-coding
Merged-chr13-94014755-1	chr13	94014672	94014839	+	1	NA	Intergenic	L1Md_A|LINE|L1	-43041	NM_172589	218454	Mm.316553	NM_172589	ENSMUSG00000045312	Lhfpl2	6030465B15|AI447312|AW050335|mKIAA0206|vgim	lipoma HMGIC fusion partner-like 2	protein-coding