Mouse Genome Overview
Information concerning the continuing improvement of the mouse genome.
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The GRC is working hard to provide the best possible reference assembly for mouse. We do this by both generating multiple representations (alternate loci) for regions that are too complex to be represented by a single path. Additionally, we are releasing regional fixes known as patches. This allows users who are interested in a specific locus to get an improved representation without affecting users who need chromosome coordinate stability.
Getting Data
- GRCm38.p2 (Latest minor release from the GRC): FTP
- GRCm38 (Latest Major release from the GRC): FTP
- Alignments of MGSCv37 to GRCm38: GRC FTP
- Information on regions under review: FTP
- Annotated clone assembly problems: FTP
Next assembly update
The next assembly update (patch release 3) will be a minor update (only patches) and will happen in June 2013.
GRCm38.p2
- Release date: 15 Mar 2013
- Release type: minor
- Release notes: Minor update of the assembly. No chromosome coordinate changes were made. There are 7 new patches with this update: 6 FIX and 1 NOVEL.
- Assembly accession: GCA_000001635.4
| Name | Chr | Start | Stop |
|---|---|---|---|
| PAR | X | 169,969,759 | 170,931,299 |
| PAR | Y | 90,745,845 | 91,644,698 |
| Sequence IDs | Assembly Unit | Region Name | Chr | Start | Stop | Patch Type |
|---|---|---|---|---|---|---|
| GL455989.1 | NT_095534.1 | BALB/c | Hbb_cluster | 7 | 103,811,478 | 103,860,690 | na |
| GL455990.1 | NT_039593.1 | A/J | Naip2_Naip5 | 13 | 100,075,065 | 100,330,017 | na |
| GL455991.1 | NT_039192.2 | 129S6/SvEvTac | Ren2 | 1 | 133,239,136 | 133,489,442 | na |
| GL455992.2 | NT_039194.5 | 129S6/SvEvTac | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| GL455993.1 | NT_039198.1 | 129S6/SvEvTac | region4 | 1 | 78,413,759 | 78,687,489 | na |
| GL455994.1 | NT_039291.1 | 129S6/SvEvTac | Prame_region_1 | 4 | 144,179,444 | 144,348,902 | na |
| GL455995.1 | NT_039334.1 | 129S6/SvEvTac | region45 | 5 | 150,872,255 | 151,123,781 | na |
| GL455996.1 | NT_039469.1 | 129S6/SvEvTac | region54 | 8 | 41,292,834 | 41,482,533 | na |
| GL455997.1 | NT_039470.1 | 129S6/SvEvTac | Large | 8 | 73,065,642 | 73,319,050 | na |
| GL455998.1 | NT_078683.1 | 129S6/SvEvTac | olfactory_region_1 | 11 | 58,613,181 | 58,787,285 | na |
| GL455999.2 | NT_039594.3 | 129S6/SvEvTac | Ipo11 | 13 | 106,801,073 | 106,932,896 | na |
| GL456000.1 | NT_039622.1 | 129S6/SvEvTac | region19 | 15 | 80,502,872 | 80,672,368 | na |
| GL456001.2 | NT_039634.4 | 129S6/SvEvTac | DownSynCrit_region_1 | 16 | 94,114,272 | 95,747,459 | na |
| GL456002.2 | NT_039666.2 | 129S6/SvEvTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456003.2 | NT_039739.2 | 129S6/SvEvTac | Odz1 | X | 42,891,057 | 43,298,842 | na |
| GL456004.1 | NT_099024.1 | 129S6/SvEvTac | Xlr_region_1 | X | 73,003,651 | 73,121,964 | na |
| GL456005.1 | NT_039195.1 | 129X1/SvJ | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| GL456006.1 | NT_039248.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456007.1 | NT_039256.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456008.1 | NT_080257.1 | 129S1/SvImJ | Tdpoz_cluster | 3 | 93,583,858 | 93,685,263 | na |
| GL456009.1 | NT_109318.2 | UNKNOWN | Padi_cluster | 4 | 140,721,097 | 140,961,448 | na |
| GL456010.1 | NT_039296.1 | 129X1/SvJ | olfactory_region_2 | 4 | 43,762,692 | 43,857,014 | na |
| GL456011.1 | NT_109599.1 | 129S1/SvImJ | region44 | 5 | 90,653,128 | 90,826,761 | na |
| GL456012.2 | NT_039372.2 | 129X1/SvJ | region47 | 6 | 82,734,575 | 83,039,841 | na |
| GL456013.1 | NT_039443.1 | 129S2/SvPas | olfactory_region_3 | 7 | 106,888,710 | 106,927,250 | na |
| GL456014.1 | NT_078572.1 | 129S1/SvImJ | region51 | 7 | 27,743,215 | 27,826,849 | na |
| GL456015.1 | NT_078651.1 | UNKNOWN | Grm1 | 10 | 10,861,646 | 10,927,384 | na |
| GL456016.1 | NT_039525.1 | 129X1/SvJ | Mapt | 11 | 104,203,258 | 104,362,532 | na |
| GL456017.2 | NT_114985.3 | 129S1/SvImJ | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456019.1 | NT_039614.1 | 129S1/SvImJ | Tcra_Tcrd | 14 | 52,352,473 | 54,229,076 | na |
| GL456020.1 | NT_096797.1 | 129X1/SvJ | region17 | 14 | 51,863,012 | 51,973,562 | na |
| GL456021.2 | NT_039661.4 | 129S6/SvEvTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456022.2 | NT_039662.3 | 129X1/SvJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456024.2 | NT_039223.3 | 129S1/SvImJ | region29 | 2 | 102,983,310 | 103,388,989 | na |
| GL456025.1 | NT_039373.1 | 129S1/SvImJ | region46 | 6 | 50,779,502 | 50,919,227 | na |
| GL456026.2 | NT_039382.4 | 129S1/SvImJ | region49 | 6 | 120,377,222 | 121,015,201 | na |
| GL456028.2 | NT_039630.5 | 129X1/SvJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| GL456031.1 | NT_111920.1 | 129S1/SvImJ | Xic | X | 103,589,284 | 103,841,870 | na |
| GL456032.1 | NT_039744.2 | 129S1/SvImJ | region57 | X | 72,166,181 | 72,363,206 | na |
| GL456033.2 | NT_039747.4 | 129S1/SvImJ | Xlr_region_2 | X | 73,185,425 | 73,263,090 | na |
| GL456042.2 | NT_114257.4 | NOD/MrkTac | NOD_mouse_Idd18.1 | 3 | 109,116,720 | 109,807,685 | na |
| GL456044.2 | NT_166287.2 | NOD/MrkTac | NOD_mouse_Idd18.2 | 3 | 103,590,378 | 104,055,839 | na |
| GL456045.2 | NT_039247.2 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456048.1 | NT_039252.1 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456049.2 | NT_039257.4 | NOD/MrkTac | region31 | 3 | 47,447,005 | 47,679,964 | na |
| GL456050.1 | NT_080256.1 | NOD/MrkTac | unaligned | Un | not aligned | not aligned | na |
| GL456053.2 | NT_166299.2 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146,068,508 | 151,320,022 | na |
| GL456054.2 | NT_166305.2 | NOD/ShiLtJ | NOD_mouse_Idd6.1+2 | 6 | 143,536,594 | 149,568,188 | na |
| GL456060.2 | NT_166317.2 | NOD/MrkTac | NOD_mouse_Idd4.2 | 11 | 72,908,911 | 74,370,562 | na |
| GL456064.1 | NT_039292.1 | UNKNOWN | region40 | 4 | 67,057,602 | 67,195,172 | na |
| GL456065.1 | NT_039367.1 | 129X1/SvJ | vomeronasal_region_1 | 6 | 89,851,149 | 90,290,463 | na |
| GL456068.1 | NT_096355.1 | BALB/c | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456069.1 | NT_097336.1 | UNKNOWN | Airn | 17 | 12,729,292 | 12,861,171 | na |
| GL456070.1 | NT_165784.1 | RIII | Impact | 18 | 11,238,883 | 11,458,280 | na |
| GL456071.1 | NT_166396.1 | CAST/Ei | unaligned | Y | not aligned | not aligned | na |
| GL456072.1 | NT_166398.1 | CAST/Ei | unaligned | Y | not aligned | not aligned | na |
| GL456073.1 | NT_166399.1 | CAST/Ei | unaligned | Y | not aligned | not aligned | na |
| GL456074.1 | NT_114988.1 | 129S1/SvImJ | Serpin_region_1 | 12 | 103,722,705 | 103,922,810 | na |
| GL456075.1 | NT_166293.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_1 | 4 | 61,778,759 | 62,041,201 | na |
| GL456076.1 | NT_166294.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_2 | 4 | 62,045,255 | 62,237,529 | na |
| GL456077.1 | NT_166295.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60,374,393 | 61,285,346 | na |
| GL456078.1 | NT_166322.1 | 129S7/SvEvBrd-Hprt-b-m2 | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456079.1 | NT_039697.1 | 129P2/OlaHsd | region28 | 19 | 5,679,043 | 5,707,799 | na |
| GL456080.1 | NT_166394.1 | AKR/J | unaligned | Y | not aligned | not aligned | na |
| GL456081.1 | NT_166397.1 | AKR/J | unaligned | Y | not aligned | not aligned | na |
| GL456082.1 | NT_166400.1 | AKR/J | unaligned | Y | not aligned | not aligned | na |
| GL456349.1 | NT_166433.1 | RIII | Tcl1_region_1 | 12 | 105,147,714 | 105,196,166 | na |
| JH584264.1 | NT_187002.1 | NOD/ShiLtJ | NOD_mouse_Idd6.3 | 6 | 129,636,567 | 130,656,471 | na |
| JH584265.1 | NT_187003.1 | NOD/ShiLtJ | NOD_mouse_Idd4.2Q | 11 | 86,869,779 | 89,954,755 | na |
| JH584266.1 | NT_187004.1 | NOD/ShiLtJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584267.1 | NT_187005.1 | NOD/ShiLtJ | NOD_mouse_Idd16.1 | 17 | 27,313,323 | 29,215,977 | na |
| JH584268.1 | NT_186999.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60,374,393 | 61,285,346 | na |
| JH584269.1 | NT_187000.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_3 | 4 | 59,870,283 | 60,154,907 | na |
| JH584270.1 | NT_187001.1 | 129S7/SvEvBrd-Hprt-b-m2 | region65 | 15 | 79,892,564 | 79,986,558 | na |
| JH584305.1 | NT_187006.1 | 129S1/SvImJ | Naip2_Naip5 | 13 | 100,075,065 | 100,330,017 | na |
| JH584306.1 | NT_187007.1 | 129S1/SvImJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584307.1 | NT_187008.1 | 129S1/SvImJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584308.1 | NT_187010.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584309.1 | NT_187011.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584310.1 | NT_187012.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584311.1 | NT_187013.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584312.1 | NT_187014.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584313.1 | NT_187015.1 | 129S6/SvEvTac | DownSynCrit_region_2 | 16 | 95,846,204 | 96,221,063 | na |
| JH584314.1 | NT_187016.1 | 129S6/SvEvTac | DownSynCrit_region_3 | 16 | 97,054,368 | 97,223,607 | na |
| JH584315.1 | NT_187017.1 | 129X1/SvJ | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| JH584316.1 | NT_187028.1 | CAST/Ei | region60 | 11 | 48,799,134 | 49,141,362 | na |
| JH584317.1 | NT_187029.1 | CAST/Ei | region61 | 11 | 58,115,562 | 58,302,084 | na |
| JH584318.1 | NT_187030.1 | CAST/Ei | region70 | 18 | 60,125,920 | 60,496,981 | na |
| JH584319.1 | NT_187018.1 | UNKNOWN | Slc1a1 | 19 | 28,892,559 | 28,918,752 | na |
| JH584320.1 | NT_187019.1 | NOD/MrkTac | NOD_mouse_Idd5.1 | 1 | 60,640,809 | 63,588,262 | na |
| JH584321.1 | NT_187020.1 | NOD/MrkTac | NOD_mouse_Idd5.3 | 1 | 65,597,865 | 69,265,254 | na |
| JH584322.1 | NT_187021.1 | NOD/MrkTac | NOD_mouse_Idd5.4 | 1 | 130,311,064 | 130,653,047 | na |
| JH584323.1 | NT_187022.1 | NOD/MrkTac | NOD_mouse_Idd10.1 | 3 | 99,953,865 | 101,307,585 | na |
| JH584324.1 | NT_187023.1 | NOD/MrkTac | NOD_mouse_Idd9.1 | 4 | 128,397,119 | 131,686,709 | na |
| JH584325.1 | NT_187024.1 | NOD/MrkTac | NOD_mouse_Idd9.1M | 4 | 135,021,547 | 135,237,421 | na |
| JH584326.1 | NT_187025.1 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146,068,508 | 151,320,022 | na |
| JH584327.1 | NT_187026.1 | NOD/MrkTac | NOD_mouse_Idd4.1 | 11 | 69,895,472 | 71,298,870 | na |
| JH584328.1 | NT_187027.1 | NOD/MrkTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH590470.1 | NT_187009.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH792826.1 | NW_004058050.1 | PATCHES | region71 | 4 | 143,214,657 | 143,582,942 | fix |
| JH792827.1 | NW_004058051.1 | PATCHES | region75 | 5 | 15,457,667 | 15,635,395 | fix |
| JH792828.1 | NW_004058052.1 | PATCHES | region72 | 7 | 3,000,001 | 3,475,222 | fix |
| JH792829.1 | NW_004058053.1 | PATCHES | Impact | 18 | 11,238,883 | 11,458,280 | fix |
| JH792830.1 | NW_004058054.1 | PATCHES | Tmem134 | 19 | 4,013,986 | 4,260,737 | fix |
| JH792831.1 | NW_004058055.1 | PATCHES | region77 | X | 37,804,742 | 37,986,547 | fix |
| JH792832.1 | NW_004058056.1 | PATCHES | region73 | Y | 45,842,743 | 46,337,667 | fix |
| JH792833.1 | NW_004058057.1 | PATCHES | region74 | Y | 66,019,703 | 66,188,541 | fix |
| JH792834.1 | NW_004058058.1 | PATCHES | region76 | Y | 49,216,909 | 49,556,418 | fix |
| KB469738.1 | NW_004450259.1 | PATCHES | Nlrp4g | 9 | 124,268,539 | 124,441,019 | fix |
| KB469739.1 | NW_004450260.1 | PATCHES | NOD_mouse_Idd4.2Q | 11 | 86,869,779 | 89,954,755 | fix |
| KB469740.1 | NW_004450261.1 | PATCHES | Meg3 | 12 | 109,373,903 | 109,689,534 | fix |
| KB469741.1 | NW_004450262.1 | PATCHES | DiGeorge | 16 | 17,742,495 | 19,065,968 | fix |
| KB469742.1 | NW_004450263.1 | PATCHES | region78 | 17 | 54,687,402 | 55,747,384 | fix |
GRCm38
- Release data: 23 Jan 2012
- Release type: major
- Release notes: Major update made the to last MGSC release. All chromosome coordinates have changed. There is now some representation of the PAR regions on the X and Y chromosomes. Additionally, we had to drop the Spretus alternate assembly unit to conform to GenBank guidelines.
- Assembly accession: GCA_000001635.2/GCF_000001635.20
| Name | Chr | Start | Stop |
|---|---|---|---|
| PAR | X | 169,969,759 | 170,931,299 |
| PAR | Y | 90,745,845 | 91,644,698 |
| Sequence IDs | Assembly Unit | Region Name | Chr | Start | Stop | Patch Type |
|---|---|---|---|---|---|---|
| GL455989.1 | NT_095534.1 | BALB/c | Hbb_cluster | 7 | 103,811,478 | 103,860,690 | na |
| GL455990.1 | NT_039593.1 | A/J | Naip2_Naip5 | 13 | 100,075,065 | 100,330,017 | na |
| GL455991.1 | NT_039192.2 | 129S6/SvEvTac | Ren2 | 1 | 133,239,136 | 133,489,442 | na |
| GL455992.2 | NT_039194.5 | 129S6/SvEvTac | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| GL455993.1 | NT_039198.1 | 129S6/SvEvTac | region4 | 1 | 78,413,759 | 78,687,489 | na |
| GL455994.1 | NT_039291.1 | 129S6/SvEvTac | Prame_region_1 | 4 | 144,179,444 | 144,348,902 | na |
| GL455995.1 | NT_039334.1 | 129S6/SvEvTac | region45 | 5 | 150,872,255 | 151,123,781 | na |
| GL455996.1 | NT_039469.1 | 129S6/SvEvTac | region54 | 8 | 41,292,834 | 41,482,533 | na |
| GL455997.1 | NT_039470.1 | 129S6/SvEvTac | Large | 8 | 73,065,642 | 73,319,050 | na |
| GL455998.1 | NT_078683.1 | 129S6/SvEvTac | olfactory_region_1 | 11 | 58,613,181 | 58,787,285 | na |
| GL455999.2 | NT_039594.3 | 129S6/SvEvTac | Ipo11 | 13 | 106,801,073 | 106,932,896 | na |
| GL456000.1 | NT_039622.1 | 129S6/SvEvTac | region19 | 15 | 80,502,872 | 80,672,368 | na |
| GL456001.2 | NT_039634.4 | 129S6/SvEvTac | DownSynCrit_region_1 | 16 | 94,114,272 | 95,747,459 | na |
| GL456002.2 | NT_039666.2 | 129S6/SvEvTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456003.2 | NT_039739.2 | 129S6/SvEvTac | Odz1 | X | 42,891,057 | 43,298,842 | na |
| GL456004.1 | NT_099024.1 | 129S6/SvEvTac | Xlr_region_1 | X | 73,003,651 | 73,121,964 | na |
| GL456005.1 | NT_039195.1 | 129X1/SvJ | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| GL456006.1 | NT_039248.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456007.1 | NT_039256.1 | 129S1/SvImJ | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456008.1 | NT_080257.1 | 129S1/SvImJ | Tdpoz_cluster | 3 | 93,583,858 | 93,685,263 | na |
| GL456009.1 | NT_109318.2 | UNKNOWN | Padi_cluster | 4 | 140,721,097 | 140,961,448 | na |
| GL456010.1 | NT_039296.1 | 129X1/SvJ | olfactory_region_2 | 4 | 43,762,692 | 43,857,014 | na |
| GL456011.1 | NT_109599.1 | 129S1/SvImJ | region44 | 5 | 90,653,128 | 90,826,761 | na |
| GL456012.2 | NT_039372.2 | 129X1/SvJ | region47 | 6 | 82,734,575 | 83,039,841 | na |
| GL456013.1 | NT_039443.1 | 129S2/SvPas | olfactory_region_3 | 7 | 106,888,710 | 106,927,250 | na |
| GL456014.1 | NT_078572.1 | 129S1/SvImJ | region51 | 7 | 27,743,215 | 27,826,849 | na |
| GL456015.1 | NT_078651.1 | UNKNOWN | Grm1 | 10 | 10,861,646 | 10,927,384 | na |
| GL456016.1 | NT_039525.1 | 129X1/SvJ | Mapt | 11 | 104,203,258 | 104,362,532 | na |
| GL456017.2 | NT_114985.3 | 129S1/SvImJ | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456019.1 | NT_039614.1 | 129S1/SvImJ | Tcra_Tcrd | 14 | 52,352,473 | 54,229,076 | na |
| GL456020.1 | NT_096797.1 | 129X1/SvJ | region17 | 14 | 51,863,012 | 51,973,562 | na |
| GL456021.2 | NT_039661.4 | 129S6/SvEvTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456022.2 | NT_039662.3 | 129X1/SvJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| GL456024.2 | NT_039223.3 | 129S1/SvImJ | region29 | 2 | 102,983,310 | 103,388,989 | na |
| GL456025.1 | NT_039373.1 | 129S1/SvImJ | region46 | 6 | 50,779,502 | 50,919,227 | na |
| GL456026.2 | NT_039382.4 | 129S1/SvImJ | region49 | 6 | 120,377,222 | 121,015,201 | na |
| GL456028.2 | NT_039630.5 | 129X1/SvJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| GL456031.1 | NT_111920.1 | 129S1/SvImJ | Xic | X | 103,589,284 | 103,841,870 | na |
| GL456032.1 | NT_039744.2 | 129S1/SvImJ | region57 | X | 72,166,181 | 72,363,206 | na |
| GL456033.2 | NT_039747.4 | 129S1/SvImJ | Xlr_region_2 | X | 73,185,425 | 73,263,090 | na |
| GL456042.2 | NT_114257.4 | NOD/MrkTac | NOD_mouse_Idd18.1 | 3 | 109,116,720 | 109,807,685 | na |
| GL456044.2 | NT_166287.2 | NOD/MrkTac | NOD_mouse_Idd18.2 | 3 | 103,590,378 | 104,055,839 | na |
| GL456045.2 | NT_039247.2 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456048.1 | NT_039252.1 | NOD/MrkTac | NOD_mouse_Idd3.1 | 3 | 36,806,723 | 37,563,603 | na |
| GL456049.2 | NT_039257.4 | NOD/MrkTac | region31 | 3 | 47,447,005 | 47,679,964 | na |
| GL456053.2 | NT_166299.2 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146,068,508 | 151,320,022 | na |
| GL456054.2 | NT_166305.2 | NOD/ShiLtJ | NOD_mouse_Idd6.1+2 | 6 | 143,536,594 | 149,568,188 | na |
| GL456060.2 | NT_166317.2 | NOD/MrkTac | NOD_mouse_Idd4.2 | 11 | 72,908,911 | 74,370,562 | na |
| GL456064.1 | NT_039292.1 | UNKNOWN | region40 | 4 | 67,057,602 | 67,195,172 | na |
| GL456065.1 | NT_039367.1 | 129X1/SvJ | vomeronasal_region_1 | 6 | 89,851,149 | 90,290,463 | na |
| GL456068.1 | NT_096355.1 | BALB/c | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456069.1 | NT_097336.1 | UNKNOWN | Airn | 17 | 12,729,292 | 12,861,171 | na |
| GL456070.1 | NT_165784.1 | RIII | Impact | 18 | 11,308,625 | 11,318,460 | na |
| GL456074.1 | NT_114988.1 | 129S1/SvImJ | Serpin_region_1 | 12 | 103,722,705 | 103,922,810 | na |
| GL456075.1 | NT_166293.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_1 | 4 | 61,778,759 | 62,041,201 | na |
| GL456076.1 | NT_166294.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_2 | 4 | 62,045,255 | 62,237,529 | na |
| GL456077.1 | NT_166295.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60,374,393 | 61,285,346 | na |
| GL456078.1 | NT_166322.1 | 129S7/SvEvBrd-Hprt-b-m2 | Igh | 12 | 113,067,904 | 114,458,697 | na |
| GL456079.1 | NT_039697.1 | 129P2/OlaHsd | region28 | 19 | 5,679,043 | 5,707,799 | na |
| GL456349.1 | NT_166433.1 | RIII | Tcl1_region_1 | 12 | 105,147,714 | 105,196,166 | na |
| JH584264.1 | NT_187002.1 | NOD/ShiLtJ | NOD_mouse_Idd6.3 | 6 | 129,636,567 | 130,656,471 | na |
| JH584265.1 | NT_187003.1 | NOD/ShiLtJ | NOD_mouse_Idd4.2Q | 11 | 86,869,779 | 89,954,755 | na |
| JH584266.1 | NT_187004.1 | NOD/ShiLtJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584267.1 | NT_187005.1 | NOD/ShiLtJ | NOD_mouse_Idd16.1 | 17 | 27,313,323 | 29,215,977 | na |
| JH584268.1 | NT_186999.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_4 | 4 | 60,374,393 | 61,285,346 | na |
| JH584269.1 | NT_187000.1 | 129S7/SvEvBrd-Hprt-b-m2 | Mup_region_3 | 4 | 59,870,283 | 60,154,907 | na |
| JH584270.1 | NT_187001.1 | 129S7/SvEvBrd-Hprt-b-m2 | region65 | 15 | 79,892,564 | 79,986,558 | na |
| JH584305.1 | NT_187006.1 | 129S1/SvImJ | Naip2_Naip5 | 13 | 100,075,065 | 100,330,017 | na |
| JH584306.1 | NT_187007.1 | 129S1/SvImJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584307.1 | NT_187008.1 | 129S1/SvImJ | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584308.1 | NT_187010.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584309.1 | NT_187011.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH584310.1 | NT_187012.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584311.1 | NT_187013.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584312.1 | NT_187014.1 | 129S6/SvEvTac | DiGeorge | 16 | 17,742,495 | 19,065,968 | na |
| JH584313.1 | NT_187015.1 | 129S6/SvEvTac | DownSynCrit_region_2 | 16 | 95,846,204 | 96,221,063 | na |
| JH584314.1 | NT_187016.1 | 129S6/SvEvTac | DownSynCrit_region_3 | 16 | 97,054,368 | 97,223,607 | na |
| JH584315.1 | NT_187017.1 | 129X1/SvJ | Ifi_cluster | 1 | 173,701,136 | 174,051,183 | na |
| JH584316.1 | NT_187028.1 | CAST/Ei | region60 | 11 | 48,799,134 | 49,141,362 | na |
| JH584317.1 | NT_187029.1 | CAST/Ei | region61 | 11 | 58,115,562 | 58,302,084 | na |
| JH584318.1 | NT_187030.1 | CAST/Ei | region70 | 18 | 60,125,920 | 60,496,981 | na |
| JH584319.1 | NT_187018.1 | UNKNOWN | Slc1a1 | 19 | 28,892,559 | 28,918,752 | na |
| JH584320.1 | NT_187019.1 | NOD/MrkTac | NOD_mouse_Idd5.1 | 1 | 60,640,809 | 63,588,262 | na |
| JH584321.1 | NT_187020.1 | NOD/MrkTac | NOD_mouse_Idd5.3 | 1 | 65,597,865 | 69,265,254 | na |
| JH584322.1 | NT_187021.1 | NOD/MrkTac | NOD_mouse_Idd5.4 | 1 | 130,311,064 | 130,653,047 | na |
| JH584323.1 | NT_187022.1 | NOD/MrkTac | NOD_mouse_Idd10.1 | 3 | 99,953,865 | 101,307,585 | na |
| JH584324.1 | NT_187023.1 | NOD/MrkTac | NOD_mouse_Idd9.1 | 4 | 128,397,119 | 131,686,709 | na |
| JH584325.1 | NT_187024.1 | NOD/MrkTac | NOD_mouse_Idd9.1M | 4 | 135,021,547 | 135,237,421 | na |
| JH584326.1 | NT_187025.1 | NOD/MrkTac | NOD_mouse_Idd9.2_Idd9.3 | 4 | 146,068,508 | 151,320,022 | na |
| JH584327.1 | NT_187026.1 | NOD/MrkTac | NOD_mouse_Idd4.1 | 11 | 69,895,472 | 71,298,870 | na |
| JH584328.1 | NT_187027.1 | NOD/MrkTac | MHC | 17 | 33,681,276 | 38,548,659 | na |
| JH590470.1 | NT_187009.1 | 129S1/SvImJ | MHC | 17 | 33,681,276 | 38,548,659 | na |
MGSCv37
- Release date: 10 Jul 2007
- Release type: major
- Release notes: Last assembly released by the MGSC. The GRC has updated the assembly structure so that it resembles human. This means the alternate loci (sequence from other strains) have been aligned to the chromosome and put into a chromosome context. Some alternate loci that were very similar to C57BL/6J were dropped, but no changes were made to the C57BL/6J part of the assemlby. This assembly was also submitted to GenBank.
- Assembly accession: GCA_000001635.1/GCF_000001635.18
| Name | Chr | Start | Stop |
|---|
| Sequence IDs | Assembly Unit | Region Name | Chr | Start | Stop | Patch Type |
|---|---|---|---|---|---|---|
| GL455989.1 | NT_095534.1 | Balb/c | Hbb_cluster | 7 | 110,959,995 | 111,009,204 | na |
| GL455990.1 | NT_039593.1 | A/J | Naip2_Naip5 | 13 | 100,922,006 | 101,021,810 | na |
| GL455991.1 | NT_039192.2 | 129/SvEvTac | Ren2 | 1 | 135,135,713 | 135,386,019 | na |
| GL455992.1 | NT_039194.4 | 129/SvEvTac | Ifi_cluster | 1 | 175,631,261 | 175,981,314 | na |
| GL455993.1 | NT_039198.1 | 129/SvEvTac | region4 | 1 | 78,410,334 | 78,684,064 | na |
| GL455995.1 | NT_039334.1 | 129/SvEvTac | region45 | 5 | 151,674,830 | 151,925,798 | na |
| GL455996.1 | NT_039469.1 | 129/SvEvTac | region54 | 8 | 42,378,188 | 42,567,887 | na |
| GL455997.1 | NT_039470.1 | 129/SvEvTac | Large | 8 | 75,589,541 | 75,842,949 | na |
| GL455998.1 | NT_078683.1 | 129/SvEvTac | olfactory_region_1 | 11 | 58,426,683 | 58,600,787 | na |
| GL455999.1 | NT_039594.2 | 129/SvEvTac | Ipo11 | 13 | 107,591,153 | 107,722,976 | na |
| GL456000.1 | NT_039622.1 | 129/SvEvTac | region19 | 15 | 80,333,302 | 80,502,798 | na |
| GL456001.1 | NT_039634.3 | 129/SvEvTac | DownSynCrit | 16 | 94,114,517 | 95,701,295 | na |
| GL456002.1 | NT_039666.1 | 129/SvEvTac | MHC_region_2 | 17 | 36,230,820 | 38,050,373 | na |
| GL456003.1 | NT_039739.1 | 129/SvEvTac | Odz1 | X | 40,330,809 | 40,652,019 | na |
| GL456004.1 | NT_099024.1 | 129/SvEvTac | Xlr_region_1 | X | 70,248,990 | 70,367,303 | na |
| GL456005.1 | NT_039195.1 | 129/SvJ | Ifi_cluster | 1 | 175,631,261 | 175,981,314 | na |
| GL456006.1 | NT_039248.1 | 129/SvJ | region30 | 3 | 36,705,645 | 37,462,525 | na |
| GL456007.1 | NT_039256.1 | 129/SvJ | region30 | 3 | 36,705,645 | 37,462,525 | na |
| GL456009.1 | NT_109318.2 | 129/SvJ | Padi_cluster | 4 | 140,277,012 | 140,517,363 | na |
| GL456010.1 | NT_039296.1 | 129/SvJ | olfactory_region_2 | 4 | 43,775,564 | 43,869,886 | na |
| GL456011.1 | NT_109599.1 | 129/SvJ | region44 | 5 | 91,082,154 | 91,255,787 | na |
| GL456012.1 | NT_039372.1 | 129/SvJ | region47 | 6 | 82,834,040 | 82,989,835 | na |
| GL456013.1 | NT_039443.1 | 129/SvJ | olfactory_region_3 | 7 | 114,032,224 | 114,070,764 | na |
| GL456014.1 | NT_078572.1 | 129/SvJ | region51 | 7 | 28,528,234 | 28,611,868 | na |
| GL456015.1 | NT_078651.1 | 129/SvJ | Grm1 | 10 | 10,581,444 | 10,647,182 | na |
| GL456016.1 | NT_039525.1 | 129/SvJ | Mapt | 11 | 104,064,572 | 104,223,846 | na |
| GL456017.1 | NT_114985.2 | 129/SvJ | Igh | 12 | 105,978,478 | 115,696,908 | na |
| GL456018.1 | NT_039572.1 | 129/SvJ | Igh | 12 | 105,978,478 | 115,696,908 | na |
| GL456019.1 | NT_039614.1 | 129/SvJ | Tcra_Tcrd | 14 | 52,971,974 | 54,848,751 | na |
| GL456020.1 | NT_096797.1 | 129/SvJ | region17 | 14 | 52,482,687 | 52,593,237 | na |
| GL456021.1 | NT_039661.3 | 129/SvJ | MHC_region_2 | 17 | 36,230,820 | 38,050,373 | na |
| GL456022.1 | NT_039662.2 | 129/SvJ | MHC_region_1 | 17 | 33,888,191 | 35,744,546 | na |
| GL456023.1 | NT_039663.1 | 129/SvJ | MHC_region_1 | 17 | 33,888,191 | 35,744,546 | na |
| GL456024.1 | NT_039223.2 | 129/Sv | region29 | 2 | 102,863,803 | 103,229,146 | na |
| GL456025.1 | NT_039373.1 | 129/Sv | region46 | 6 | 50,729,501 | 50,869,226 | na |
| GL456026.1 | NT_039382.3 | 129/Sv | region49 | 6 | 120,327,240 | 120,965,219 | na |
| GL456027.1 | NT_039613.3 | 129/Sv | Fhit | 14 | 11,148,176 | 11,650,860 | na |
| GL456028.1 | NT_039630.4 | 129/Sv | DiGeorge | 16 | 17,742,588 | 19,066,061 | na |
| GL456030.1 | NT_039665.1 | 129/Sv | MHC_region_2 | 17 | 36,230,820 | 38,050,373 | na |
| GL456031.1 | NT_111920.1 | 129/Sv | Xic | X | 100,784,623 | 101,037,209 | na |
| GL456032.1 | NT_039744.2 | 129/Sv | region57 | X | 69,411,520 | 69,608,545 | na |
| GL456033.1 | NT_039747.3 | 129/Sv | Xlr_region_2 | X | 70,430,764 | 70,508,135 | na |
| GL456036.1 | NT_165757.1 | NOD | region1 | 1 | 60,697,653 | 61,195,514 | na |
| GL456037.1 | NT_039197.1 | NOD | region2 | 1 | 61,754,170 | 61,941,338 | na |
| GL456038.1 | NT_039199.1 | NOD | region1 | 1 | 60,697,653 | 61,195,514 | na |
| GL456039.1 | NT_039200.1 | NOD | region1 | 1 | 60,697,653 | 61,195,514 | na |
| GL456040.1 | NT_039201.1 | NOD | region3 | 1 | 63,440,029 | 63,634,836 | na |
| GL456041.1 | NT_109311.1 | NOD | region32 | 3 | 99,757,788 | 99,890,338 | na |
| GL456042.1 | NT_114257.3 | NOD | region36 | 3 | 108,919,638 | 109,610,603 | na |
| GL456044.1 | NT_166287.1 | NOD | region35 | 3 | 103,394,301 | 103,719,496 | na |
| GL456045.1 | NT_039247.1 | NOD | region30 | 3 | 36,705,645 | 37,462,525 | na |
| GL456046.1 | NT_039250.1 | NOD | region33 | 3 | 100,124,682 | 100,629,140 | na |
| GL456047.1 | NT_039251.2 | NOD | region34 | 3 | 100,709,803 | 101,111,508 | na |
| GL456048.1 | NT_039252.1 | NOD | region30 | 3 | 36,705,645 | 37,462,525 | na |
| GL456049.1 | NT_039257.3 | NOD | region31 | 3 | 47,250,927 | 47,483,886 | na |
| GL456051.1 | NT_166297.1 | NOD | region42 | 4 | 129,673,209 | 129,813,999 | na |
| GL456052.1 | NT_166298.1 | NOD | region41 | 4 | 129,222,696 | 129,387,052 | na |
| GL456054.1 | NT_166305.1 | NOD | region50 | 6 | 144,953,971 | 145,181,710 | na |
| GL456055.1 | NT_110625.3 | NOD | region9 | 11 | 69,708,974 | 70,768,432 | na |
| GL456056.1 | NT_110626.2 | NOD | region9 | 11 | 69,708,974 | 70,768,432 | na |
| GL456057.1 | NT_114882.1 | NOD | region11 | 11 | 88,404,152 | 88,462,832 | na |
| GL456059.1 | NT_165774.1 | NOD | region9 | 11 | 69,708,974 | 70,768,432 | na |
| GL456060.1 | NT_166317.1 | NOD | region10 | 11 | 72,722,413 | 72,881,612 | na |
| GL456061.1 | NT_165781.2 | NOD | region24 | 17 | 27,792,385 | 29,352,922 | na |
| GL456062.1 | NT_165782.2 | NOD | region24 | 17 | 27,792,385 | 29,352,922 | na |
| GL456063.1 | NT_166329.1 | NOD | region23 | 17 | 27,450,268 | 27,705,657 | na |
| GL456064.1 | NT_039292.1 | unknown strain | region40 | 4 | 66,718,636 | 66,856,206 | na |
| GL456065.1 | NT_039367.1 | unknown strain | vomeronasal_region_1 | 6 | 90,040,061 | 90,240,457 | na |
| GL456066.1 | NT_166319.1 | unknown strain | Igh | 12 | 105,978,478 | 115,696,908 | na |
| GL456067.1 | NT_166320.1 | unknown strain | Igh | 12 | 105,978,478 | 115,696,908 | na |
| GL456069.1 | NT_097336.1 | unknown strain | Airn | 17 | 12,922,132 | 13,054,037 | na |
| GL456070.1 | NT_165784.1 | unknown strain | Impact | 18 | 11,308,623 | 11,423,912 | na |
| GL456075.1 | NT_166293.1 | 129S7/SvEv | Mup_region_1 | 4 | 60,433,222 | 61,702,235 | na |
| GL456076.1 | NT_166294.1 | 129S7/SvEv | Mup_region_2 | 4 | 61,706,289 | 61,898,563 | na |
| GL456078.1 | NT_166322.1 | 129S7/SvEv | Igh | 12 | 105,978,478 | 115,696,908 | na |
| GL456079.1 | NT_039697.1 | 129P2/OlaHsd | region28 | 19 | 5,679,043 | 5,707,799 | na |
