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Mouse Genome Overview

Information about the continuing improvement of the mouse genome

The GRC is working hard to provide the best possible reference assembly for mouse. In the mouse reference assembly, sequences in the primary assembly unit (chromosomes and unlocalized and unplaced scaffolds) come from the C57BL/6J strain. For several genomic regions that are variable between different strains, we provide alternate loci scaffolds comprised of clone-based sequences from a variety of other strains. 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.

Transitioning to GRCm38? Try the NCBI Remapping Service, which uses the same assembly-assembly alignments used by the GRC.

Next assembly update

The GRC will review data for the next assembly update in spring 2018.

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Ideogram of the latest mouse assembly, GRCm38.p6

GRCm38.p6

  • Release date: September 15, 2017
  • Release type: minor
  • Release notes: Minor update of the assembly. 24 new FIX patches, 2 updated FIX patches and 8 new NOVEL patches. The total number of patch scaffolds is now 65 FIX and 9 NOVEL.
  • Assembly accessions: GenBank: GCA_000001635.8 , RefSeq: GCF_000001635.26
Pseudoautosomal regions
Name Chr Start Stop
PAR X 169,969,759 170,931,299
PAR Y 90,745,845 91,644,698

Filter by:

Gene
Patches and alternate loci
Scaffold IDs Assembly unit Region name Chr Start Stop Type
KV575234.1 | NW_016097314.1 PATCHES Rims1 1 22,159,855 22,877,939 fix
JH584320.1 | NT_187019.1 NOD/MrkTac NOD_mouse_Idd5.1 1 60,640,809 63,588,262 alt
KK082441.1 | NW_006763128.1 PATCHES NOD_mouse_Idd5.1 1 60,640,809 63,588,262 novel
JH584321.1 | NT_187020.1 NOD/MrkTac NOD_mouse_Idd5.3 1 65,597,865 69,265,254 alt
GL455993.1 | NT_039198.1 129S6/SvEvTac region4 1 78,413,759 78,687,489 alt
JH584322.1 | NT_187021.1 NOD/MrkTac NOD_mouse_Idd5.4 1 130,311,064 130,653,047 alt
GL455991.1 | NT_039192.2 129S6/SvEvTac Ren2 1 133,239,136 133,489,442 alt
GL455992.2 | NT_039194.5 129S6/SvEvTac Ifi_cluster 1 173,701,136 174,051,183 alt
GL456005.1 | NT_039195.1 129X1/SvJ Ifi_cluster 1 173,701,136 174,051,183 alt
JH584315.1 | NT_187017.1 129X1/SvJ Ifi_cluster 1 173,701,136 174,051,183 alt
KV575232.1 | NW_016097312.1 PATCHES region86 1 178,144,751 178,344,759 fix
KV575233.1 | NW_016097313.1 PATCHES Traf5 1 191,793,213 192,106,925 fix
KV575235.1 | NW_016097315.1 PATCHES Ptpmt1 2 90,853,948 91,049,681 fix
GL456024.2 | NT_039223.3 129S1/SvImJ region29 2 102,983,310 103,388,989 alt
KV575236.1 | NW_016097316.1 PATCHES Spata5l1 2 122,566,305 122,720,961 fix
KQ030484.1 | NW_012132900.1 PATCHES region80 3 15,760,691 15,949,398 fix
GL456006.1 | NT_039248.1 129S1/SvImJ NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456007.1 | NT_039256.1 129S1/SvImJ NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456045.2 | NT_039247.2 NOD/MrkTac NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456048.1 | NT_039252.1 NOD/MrkTac NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
KZ289066.1 | NW_019168505.1 PATCHES Intu 3 40,505,691 40,944,643 fix
GL456049.2 | NT_039257.4 NOD/MrkTac region31 3 47,447,005 47,679,964 alt
KZ289065.1 | NW_019168504.1 PATCHES region87 3 50,686,235 50,904,915 fix
GL456008.1 | NT_080257.1 129S1/SvImJ Tdpoz_cluster 3 93,583,858 93,685,263 alt
JH584323.1 | NT_187022.1 NOD/MrkTac NOD_mouse_Idd10.1 3 99,953,865 101,307,585 alt
GL456044.2 | NT_166287.2 NOD/MrkTac NOD_mouse_Idd18.2 3 103,590,378 104,055,839 alt
GL456042.2 | NT_114257.4 NOD/MrkTac NOD_mouse_Idd18.1 3 109,116,720 109,807,685 alt
KZ289064.1 | NW_019168503.1 PATCHES Sgms2 3 131,299,856 131,505,512 fix
GL456010.1 | NT_039296.1 129X1/SvJ olfactory_region_2 4 43,762,692 43,857,014 alt
JH584269.1 | NT_187000.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_3 4 59,870,283 60,154,907 alt
GL456077.1 | NT_166295.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_4 4 60,250,666 61,586,638 alt
JH584268.1 | NT_186999.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_4 4 60,250,666 61,586,638 alt
KQ030485.1 | NW_012132901.1 PATCHES Mup_region_4 4 60,250,666 61,586,638 fix
KQ030486.1 | NW_012132902.1 PATCHES Mup_region_4 4 60,250,666 61,586,638 fix
GL456075.1 | NT_166293.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_1 4 61,778,759 62,041,201 alt
GL456076.1 | NT_166294.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_2 4 62,045,255 62,237,529 alt
GL456064.1 | NT_039292.1 UNKNOWN region40 4 67,057,602 67,195,172 alt
KZ289070.1 | NW_019168509.1 PATCHES Efcab7 4 99,625,547 100,035,456 fix
KZ289067.1 | NW_019168506.1 PATCHES region88 4 121,426,261 122,034,165 fix
KQ030487.1 | NW_012132903.1 PATCHES region79 4 122,217,500 122,473,817 fix
JH584324.1 | NT_187023.1 NOD/MrkTac NOD_mouse_Idd9.1 4 128,397,119 131,686,709 alt
KQ030488.1 | NW_012132904.1 PATCHES NOD_mouse_Idd9.1 4 128,397,119 131,686,709 fix
KQ030489.1 | NW_012132905.1 PATCHES NOD_mouse_Idd9.1 4 128,397,119 131,686,709 fix
JH584325.1 | NT_187024.1 NOD/MrkTac NOD_mouse_Idd9.1M 4 135,021,547 135,237,421 alt
GL456009.1 | NT_109318.2 UNKNOWN Padi_cluster 4 140,721,097 140,961,448 alt
KZ289069.1 | NW_019168508.1 PATCHES region89 4 141,987,963 142,697,802 fix
JH792826.1 | NW_004058050.1 PATCHES region71 4 143,214,657 143,582,942 fix
GL455994.1 | NT_039291.1 129S6/SvEvTac Prame_region_1 4 144,179,444 144,348,902 alt
GL456053.2 | NT_166299.2 NOD/MrkTac NOD_mouse_Idd9.2_Idd9.3 4 146,068,508 151,320,022 alt
JH584326.1 | NT_187025.1 NOD/MrkTac NOD_mouse_Idd9.2_Idd9.3 4 146,068,508 151,320,022 alt
KZ289068.1 | NW_019168507.1 PATCHES NOD_mouse_Idd9.2_Idd9.3 4 146,068,508 151,320,022 fix
JH792827.1 | NW_004058051.1 PATCHES region75 5 15,457,667 15,635,395 fix
GL456011.1 | NT_109599.1 129S1/SvImJ region44 5 90,653,128 90,826,761 alt
KV575237.1 | NW_016097317.1 PATCHES Auts2 5 131,326,290 132,550,462 fix
GL455995.1 | NT_039334.1 129S6/SvEvTac region45 5 150,872,255 151,123,781 alt
GL456025.1 | NT_039373.1 129S1/SvImJ region46 6 50,779,502 50,919,227 alt
KK082442.1 | NW_006763129.1 PATCHES Sftpb 6 72,296,717 72,451,483 fix
GL456012.2 | NT_039372.2 129X1/SvJ region47 6 82,734,575 83,039,841 alt
GL456065.1 | NT_039367.1 129X1/SvJ vomeronasal_region_1 6 89,851,149 90,290,463 alt
GL456026.2 | NT_039382.4 129S1/SvImJ region49 6 120,377,222 121,015,201 alt
JH584264.1 | NT_187002.1 NOD/ShiLtJ NOD_mouse_Idd6.3 6 129,636,567 130,656,471 alt
GL456054.2 | NT_166305.2 NOD/ShiLtJ NOD_mouse_Idd6.1+2 6 143,536,594 149,568,188 alt
JH792828.1 | NW_004058052.1 PATCHES region72 7 3,000,001 3,475,222 fix
GL456014.1 | NT_078572.1 129S1/SvImJ region51 7 27,743,215 27,826,849 alt
GL455989.1 | NT_095534.1 BALB/c Hbb_cluster 7 103,811,478 103,860,690 alt
GL456013.1 | NT_039443.1 129S2/SvPas olfactory_region_3 7 106,888,710 106,927,250 alt
KV575238.1 | NW_016097318.1 PATCHES Jakmip3 7 138,934,711 139,370,933 fix
KV575239.1 | NW_016097319.1 PATCHES Muc2 7 141,683,154 141,786,694 fix
GL455996.1 | NT_039469.1 129S6/SvEvTac region54 8 41,292,834 41,482,533 alt
KV575240.1 | NW_016097320.1 PATCHES Rab3a_Ifi30 8 70,673,831 70,845,694 fix
GL455997.1 | NT_039470.1 129S6/SvEvTac Large 8 73,065,642 73,319,050 alt
KQ030490.1 | NW_012132906.1 PATCHES Slc26a6 9 108,784,955 108,953,239 fix
KB469738.3 | NW_004450259.3 PATCHES Nlrp4g 9 124,268,539 124,479,149 fix
KZ289071.1 | NW_019168510.1 PATCHES region90 10 7,346,541 7,776,389 fix
GL456015.1 | NT_078651.1 UNKNOWN Grm1 10 10,861,646 10,927,384 alt
KQ030491.1 | NW_012132907.1 PATCHES region81 10 58,205,866 58,311,233 fix
KZ289072.1 | NW_019168511.1 PATCHES region91 10 67,228,314 67,653,670 fix
KZ289076.1 | NW_019168515.1 PATCHES region92 11 7,560,598 7,879,512 fix
JH584316.1 | NT_187028.1 CAST/Ei region60 11 48,799,134 49,141,362 alt
KZ289073.1 | NW_019168512.1 PATCHES region60 11 48,799,134 49,141,362 novel
KZ289077.1 | NW_019168516.1 PATCHES region60 11 48,799,134 49,141,362 novel
JH584317.1 | NT_187029.1 CAST/Ei region61 11 58,115,562 58,302,084 alt
GL455998.1 | NT_078683.1 129S6/SvEvTac olfactory_region_1 11 58,613,181 58,787,285 alt
JH584327.1 | NT_187026.1 NOD/MrkTac NOD_mouse_Idd4.1 11 69,895,472 71,336,724 alt
KZ289074.1 | NW_019168513.1 PATCHES NOD_mouse_Idd4.1 11 69,895,472 71,336,724 novel
KZ289078.1 | NW_019168517.1 PATCHES NOD_mouse_Idd4.1 11 69,895,472 71,336,724 novel
KZ289080.1 | NW_019168519.1 PATCHES NOD_mouse_Idd4.1 11 69,895,472 71,336,724 novel
GL456060.2 | NT_166317.2 NOD/MrkTac NOD_mouse_Idd4.2 11 72,908,911 74,370,562 alt
KZ289075.1 | NW_019168514.1 PATCHES region93 11 82,933,464 83,353,797 novel
KZ289079.1 | NW_019168518.1 PATCHES region93 11 82,933,464 83,353,797 novel
KZ289081.1 | NW_019168520.1 PATCHES region93 11 82,933,464 83,353,797 novel
JH584265.1 | NT_187003.1 NOD/ShiLtJ NOD_mouse_Idd4.2Q 11 86,869,779 89,954,755 alt
KB469739.1 | NW_004450260.1 PATCHES NOD_mouse_Idd4.2Q 11 86,869,779 89,954,755 fix
GL456016.1 | NT_039525.1 129X1/SvJ Mapt 11 104,203,258 104,362,532 alt
GL456074.1 | NT_114988.1 129S1/SvImJ Serpin_region_1 12 103,722,705 103,922,810 alt
GL456349.1 | NT_166433.1 RIII Tcl1_region_1 12 105,147,714 105,196,166 alt
KB469740.1 | NW_004450261.1 PATCHES Meg3 12 109,373,903 109,689,534 fix
KZ289082.1 | NW_019168521.1 PATCHES Ahnak2 12 112,701,299 112,815,832 fix
GL456017.2 | NT_114985.3 129S1/SvImJ Igh 12 113,067,904 114,458,697 alt
GL456068.1 | NT_096355.1 BALB/c Igh 12 113,067,904 114,458,697 alt
GL456078.1 | NT_166322.1 129S7/SvEvBrd-Hprt-b-m2 Igh 12 113,067,904 114,458,697 alt
GL455990.1 | NT_039593.1 A/J Naip2_Naip5 13 100,075,065 100,330,017 alt
JH584305.1 | NT_187006.1 129S1/SvImJ Naip2_Naip5 13 100,075,065 100,330,017 alt
GL455999.2 | NT_039594.3 129S6/SvEvTac Ipo11 13 106,801,073 106,932,896 alt
KZ289083.1 | NW_019168522.1 PATCHES region94 14 24,646,407 24,762,340 fix
KZ289084.1 | NW_019168523.1 PATCHES Dnah12 14 26,629,355 26,911,986 fix
GL456020.1 | NT_096797.1 129X1/SvJ region17 14 51,863,012 51,973,562 alt
GL456019.1 | NT_039614.1 129S1/SvImJ Tcra_Tcrd 14 52,352,473 54,229,076 alt
KQ030492.1 | NW_012132908.1 PATCHES region82 15 3,050,001 3,186,530 fix
KV575241.1 | NW_016097321.1 PATCHES Nadk2 15 9,054,779 9,266,110 fix
KQ030493.2 | NW_012132909.2 PATCHES Baalc 15 38,582,635 39,142,852 fix
KZ289086.1 | NW_019168525.1 PATCHES Anxa13 15 57,983,529 58,517,868 fix
JH584270.1 | NT_187001.1 129S7/SvEvBrd-Hprt-b-m2 region65 15 79,892,564 79,986,558 alt
GL456000.1 | NT_039622.1 129S6/SvEvTac region19 15 80,502,872 80,672,368 alt
KZ289085.1 | NW_019168524.1 PATCHES region95 15 103,658,568 103,917,132 fix
GL456028.2 | NT_039630.5 129X1/SvJ DiGeorge 16 17,742,495 19,065,968 alt
JH584306.1 | NT_187007.1 129S1/SvImJ DiGeorge 16 17,742,495 19,065,968 alt
JH584307.1 | NT_187008.1 129S1/SvImJ DiGeorge 16 17,742,495 19,065,968 alt
JH584310.1 | NT_187012.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
JH584311.1 | NT_187013.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
JH584312.1 | NT_187014.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
KB469741.2 | NW_004450262.2 PATCHES DiGeorge 16 17,742,495 19,065,968 fix
GL456001.2 | NT_039634.4 129S6/SvEvTac DownSynCrit_region_1 16 94,114,272 95,747,459 alt
JH584313.1 | NT_187015.1 129S6/SvEvTac DownSynCrit_region_2 16 95,846,204 96,221,063 alt
JH584314.1 | NT_187016.1 129S6/SvEvTac DownSynCrit_region_3 16 97,054,368 97,223,607 alt
KZ289087.1 | NW_019168526.1 PATCHES region96 17 7,391,520 7,693,199 fix
GL456069.1 | NT_097336.1 UNKNOWN Airn 17 12,729,292 12,861,171 alt
JH584267.1 | NT_187005.1 NOD/ShiLtJ NOD_mouse_Idd16.1 17 27,313,323 29,215,977 alt
GL456002.2 | NT_039666.2 129S6/SvEvTac MHC 17 33,681,276 38,548,659 alt
GL456021.2 | NT_039661.4 129S6/SvEvTac MHC 17 33,681,276 38,548,659 alt
GL456022.2 | NT_039662.3 129X1/SvJ MHC 17 33,681,276 38,548,659 alt
JH584266.1 | NT_187004.1 NOD/ShiLtJ MHC 17 33,681,276 38,548,659 alt
JH584308.1 | NT_187010.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
JH584309.1 | NT_187011.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
JH584328.1 | NT_187027.1 NOD/MrkTac MHC 17 33,681,276 38,548,659 alt
JH590470.1 | NT_187009.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
KZ289088.1 | NW_019168527.1 PATCHES Trerf1 17 47,094,952 47,423,636 fix
KZ289089.1 | NW_019168528.1 PATCHES region97 17 47,916,958 48,583,287 fix
KB469742.1 | NW_004450263.1 PATCHES region78 17 54,687,402 55,747,384 fix
GL456070.1 | NT_165784.1 RIII Impact 18 11,238,883 11,458,280 alt
JH792829.1 | NW_004058053.1 PATCHES Impact 18 11,238,883 11,458,280 fix
JH584318.1 | NT_187030.1 CAST/Ei region70 18 60,125,920 60,496,981 alt
KZ289090.1 | NW_019168529.1 PATCHES region98 18 76,466,242 76,775,534 fix
KZ289091.1 | NW_019168530.1 PATCHES Pstpip2 18 77,623,953 78,117,342 fix
JH792830.1 | NW_004058054.1 PATCHES Tmem134 19 4,013,986 4,260,737 fix
GL456079.1 | NT_039697.1 129P2/OlaHsd region28 19 5,679,043 5,707,799 alt
KQ030494.1 | NW_012132910.1 PATCHES region83 19 6,183,084 6,688,105 fix
JH584319.1 | NT_187018.1 UNKNOWN Slc1a1 19 28,892,559 28,918,752 alt
KV575242.1 | NW_016097322.1 PATCHES Ide 19 37,204,249 37,492,988 fix
KZ289093.1 | NW_019168532.1 PATCHES Dgkk X 6,763,452 7,054,396 fix
KQ030496.1 | NW_012132912.1 PATCHES region85 X 29,000,987 29,562,451 fix
KQ030497.1 | NW_012132913.1 PATCHES region85 X 29,000,987 29,562,451 fix
JH792831.2 | NW_004058055.2 PATCHES region77 X 37,690,395 37,986,547 fix
GL456003.2 | NT_039739.2 129S6/SvEvTac Odz1 X 42,891,057 43,298,842 alt
KZ289094.1 | NW_019168533.1 PATCHES 4933416I08Rik X 53,444,973 53,687,352 fix
KQ030495.1 | NW_012132911.1 PATCHES region84 X 60,271,962 60,763,715 fix
GL456032.1 | NT_039744.2 129S1/SvImJ region57 X 72,166,181 72,363,206 alt
GL456004.1 | NT_099024.1 129S6/SvEvTac Xlr_region_1 X 73,003,651 73,121,964 alt
GL456033.2 | NT_039747.4 129S1/SvImJ Xlr_region_2 X 73,185,425 73,263,090 alt
GL456031.1 | NT_111920.1 129S1/SvImJ Xic X 103,589,284 103,841,870 alt
KZ289095.1 | NW_019168534.1 PATCHES region99 X 111,104,003 111,543,375 fix
KZ289092.1 | NW_019168531.1 PATCHES Atg4a X 140,784,762 141,363,409 fix
GL456071.1 | NT_166396.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456072.1 | NT_166398.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456073.1 | NT_166399.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456080.1 | NT_166394.1 AKR/J unaligned Y not aligned not aligned alt
GL456081.1 | NT_166397.1 AKR/J unaligned Y not aligned not aligned alt
GL456082.1 | NT_166400.1 AKR/J unaligned Y not aligned not aligned alt
JH792832.1 | NW_004058056.1 PATCHES region73 Y 45,842,743 46,337,667 fix
JH792834.1 | NW_004058058.1 PATCHES region76 Y 49,216,909 49,556,418 fix
JH792833.1 | NW_004058057.1 PATCHES region74 Y 66,019,703 66,188,541 fix
KK082443.1 | NW_006763130.1 PATCHES region1a JH584264.1|NT_187002.1 709,988 1,759,414 fix
GL456050.1 | NT_080256.1 NOD/MrkTac unaligned Un not aligned not aligned alt

GRCm38

  • Release date: January 9, 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 accessions: GenBank: GCA_000001635.2, RefSeq: GCF_000001635.20
Pseudoautosomal regions
Name Chr Start Stop
PAR X 169,969,759 170,931,299
PAR Y 90,745,845 91,644,698
Patches and alternate loci
Scaffold IDs Assembly unit Region name Chr Start Stop Type
JH584320.1 | NT_187019.1 NOD/MrkTac NOD_mouse_Idd5.1 1 60,640,809 63,588,262 alt
JH584321.1 | NT_187020.1 NOD/MrkTac NOD_mouse_Idd5.3 1 65,597,865 69,265,254 alt
GL455993.1 | NT_039198.1 129S6/SvEvTac region4 1 78,413,759 78,687,489 alt
JH584322.1 | NT_187021.1 NOD/MrkTac NOD_mouse_Idd5.4 1 130,311,064 130,653,047 alt
GL455991.1 | NT_039192.2 129S6/SvEvTac Ren2 1 133,239,136 133,489,442 alt
GL455992.2 | NT_039194.5 129S6/SvEvTac Ifi_cluster 1 173,701,136 174,051,183 alt
GL456005.1 | NT_039195.1 129X1/SvJ Ifi_cluster 1 173,701,136 174,051,183 alt
JH584315.1 | NT_187017.1 129X1/SvJ Ifi_cluster 1 173,701,136 174,051,183 alt
GL456024.2 | NT_039223.3 129S1/SvImJ region29 2 102,983,310 103,388,989 alt
GL456006.1 | NT_039248.1 129S1/SvImJ NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456007.1 | NT_039256.1 129S1/SvImJ NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456045.2 | NT_039247.2 NOD/MrkTac NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456048.1 | NT_039252.1 NOD/MrkTac NOD_mouse_Idd3.1 3 36,806,723 37,563,603 alt
GL456049.2 | NT_039257.4 NOD/MrkTac region31 3 47,447,005 47,679,964 alt
GL456008.1 | NT_080257.1 129S1/SvImJ Tdpoz_cluster 3 93,583,858 93,685,263 alt
JH584323.1 | NT_187022.1 NOD/MrkTac NOD_mouse_Idd10.1 3 99,953,865 101,307,585 alt
GL456044.2 | NT_166287.2 NOD/MrkTac NOD_mouse_Idd18.2 3 103,590,378 104,055,839 alt
GL456042.2 | NT_114257.4 NOD/MrkTac NOD_mouse_Idd18.1 3 109,116,720 109,807,685 alt
GL456010.1 | NT_039296.1 129X1/SvJ olfactory_region_2 4 43,762,692 43,857,014 alt
JH584269.1 | NT_187000.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_3 4 59,870,283 60,154,907 alt
GL456077.1 | NT_166295.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_4 4 60,374,393 61,285,346 alt
JH584268.1 | NT_186999.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_4 4 60,374,393 61,285,346 alt
GL456075.1 | NT_166293.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_1 4 61,778,759 62,041,201 alt
GL456076.1 | NT_166294.1 129S7/SvEvBrd-Hprt-b-m2 Mup_region_2 4 62,045,255 62,237,529 alt
GL456064.1 | NT_039292.1 UNKNOWN region40 4 67,057,602 67,195,172 alt
JH584324.1 | NT_187023.1 NOD/MrkTac NOD_mouse_Idd9.1 4 128,397,119 131,686,709 alt
JH584325.1 | NT_187024.1 NOD/MrkTac NOD_mouse_Idd9.1M 4 135,021,547 135,237,421 alt
GL456009.1 | NT_109318.2 UNKNOWN Padi_cluster 4 140,721,097 140,961,448 alt
GL455994.1 | NT_039291.1 129S6/SvEvTac Prame_region_1 4 144,179,444 144,348,902 alt
GL456053.2 | NT_166299.2 NOD/MrkTac NOD_mouse_Idd9.2_Idd9.3 4 146,068,508 151,320,022 alt
JH584326.1 | NT_187025.1 NOD/MrkTac NOD_mouse_Idd9.2_Idd9.3 4 146,068,508 151,320,022 alt
GL456011.1 | NT_109599.1 129S1/SvImJ region44 5 90,653,128 90,826,761 alt
GL455995.1 | NT_039334.1 129S6/SvEvTac region45 5 150,872,255 151,123,781 alt
GL456025.1 | NT_039373.1 129S1/SvImJ region46 6 50,779,502 50,919,227 alt
GL456012.2 | NT_039372.2 129X1/SvJ region47 6 82,734,575 83,039,841 alt
GL456065.1 | NT_039367.1 129X1/SvJ vomeronasal_region_1 6 89,851,149 90,290,463 alt
GL456026.2 | NT_039382.4 129S1/SvImJ region49 6 120,377,222 121,015,201 alt
JH584264.1 | NT_187002.1 NOD/ShiLtJ NOD_mouse_Idd6.3 6 129,636,567 130,656,471 alt
GL456054.2 | NT_166305.2 NOD/ShiLtJ NOD_mouse_Idd6.1+2 6 143,536,594 149,568,188 alt
GL456014.1 | NT_078572.1 129S1/SvImJ region51 7 27,743,215 27,826,849 alt
GL455989.1 | NT_095534.1 BALB/c Hbb_cluster 7 103,811,478 103,860,690 alt
GL456013.1 | NT_039443.1 129S2/SvPas olfactory_region_3 7 106,888,710 106,927,250 alt
GL455996.1 | NT_039469.1 129S6/SvEvTac region54 8 41,292,834 41,482,533 alt
GL455997.1 | NT_039470.1 129S6/SvEvTac Large 8 73,065,642 73,319,050 alt
GL456015.1 | NT_078651.1 UNKNOWN Grm1 10 10,861,646 10,927,384 alt
JH584316.1 | NT_187028.1 CAST/Ei region60 11 48,799,134 49,141,362 alt
JH584317.1 | NT_187029.1 CAST/Ei region61 11 58,115,562 58,302,084 alt
GL455998.1 | NT_078683.1 129S6/SvEvTac olfactory_region_1 11 58,613,181 58,787,285 alt
JH584327.1 | NT_187026.1 NOD/MrkTac NOD_mouse_Idd4.1 11 69,895,472 71,298,870 alt
GL456060.2 | NT_166317.2 NOD/MrkTac NOD_mouse_Idd4.2 11 72,908,911 74,370,562 alt
JH584265.1 | NT_187003.1 NOD/ShiLtJ NOD_mouse_Idd4.2Q 11 86,869,779 89,954,755 alt
GL456016.1 | NT_039525.1 129X1/SvJ Mapt 11 104,203,258 104,362,532 alt
GL456074.1 | NT_114988.1 129S1/SvImJ Serpin_region_1 12 103,722,705 103,922,810 alt
GL456349.1 | NT_166433.1 RIII Tcl1_region_1 12 105,147,714 105,196,166 alt
GL456017.2 | NT_114985.3 129S1/SvImJ Igh 12 113,067,904 114,458,697 alt
GL456068.1 | NT_096355.1 BALB/c Igh 12 113,067,904 114,458,697 alt
GL456078.1 | NT_166322.1 129S7/SvEvBrd-Hprt-b-m2 Igh 12 113,067,904 114,458,697 alt
GL455990.1 | NT_039593.1 A/J Naip2_Naip5 13 100,075,065 100,330,017 alt
JH584305.1 | NT_187006.1 129S1/SvImJ Naip2_Naip5 13 100,075,065 100,330,017 alt
GL455999.2 | NT_039594.3 129S6/SvEvTac Ipo11 13 106,801,073 106,932,896 alt
GL456020.1 | NT_096797.1 129X1/SvJ region17 14 51,863,012 51,973,562 alt
GL456019.1 | NT_039614.1 129S1/SvImJ Tcra_Tcrd 14 52,352,473 54,229,076 alt
JH584270.1 | NT_187001.1 129S7/SvEvBrd-Hprt-b-m2 region65 15 79,892,564 79,986,558 alt
GL456000.1 | NT_039622.1 129S6/SvEvTac region19 15 80,502,872 80,672,368 alt
GL456028.2 | NT_039630.5 129X1/SvJ DiGeorge 16 17,742,495 19,065,968 alt
JH584306.1 | NT_187007.1 129S1/SvImJ DiGeorge 16 17,742,495 19,065,968 alt
JH584307.1 | NT_187008.1 129S1/SvImJ DiGeorge 16 17,742,495 19,065,968 alt
JH584310.1 | NT_187012.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
JH584311.1 | NT_187013.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
JH584312.1 | NT_187014.1 129S6/SvEvTac DiGeorge 16 17,742,495 19,065,968 alt
GL456001.2 | NT_039634.4 129S6/SvEvTac DownSynCrit_region_1 16 94,114,272 95,747,459 alt
JH584313.1 | NT_187015.1 129S6/SvEvTac DownSynCrit_region_2 16 95,846,204 96,221,063 alt
JH584314.1 | NT_187016.1 129S6/SvEvTac DownSynCrit_region_3 16 97,054,368 97,223,607 alt
GL456069.1 | NT_097336.1 UNKNOWN Airn 17 12,729,292 12,861,171 alt
JH584267.1 | NT_187005.1 NOD/ShiLtJ NOD_mouse_Idd16.1 17 27,313,323 29,215,977 alt
GL456002.2 | NT_039666.2 129S6/SvEvTac MHC 17 33,681,276 38,548,659 alt
GL456021.2 | NT_039661.4 129S6/SvEvTac MHC 17 33,681,276 38,548,659 alt
GL456022.2 | NT_039662.3 129X1/SvJ MHC 17 33,681,276 38,548,659 alt
JH584266.1 | NT_187004.1 NOD/ShiLtJ MHC 17 33,681,276 38,548,659 alt
JH584308.1 | NT_187010.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
JH584309.1 | NT_187011.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
JH584328.1 | NT_187027.1 NOD/MrkTac MHC 17 33,681,276 38,548,659 alt
JH590470.1 | NT_187009.1 129S1/SvImJ MHC 17 33,681,276 38,548,659 alt
GL456070.1 | NT_165784.1 RIII Impact 18 11,308,625 11,318,460 alt
JH584318.1 | NT_187030.1 CAST/Ei region70 18 60,125,920 60,496,981 alt
GL456079.1 | NT_039697.1 129P2/OlaHsd region28 19 5,679,043 5,707,799 alt
JH584319.1 | NT_187018.1 UNKNOWN Slc1a1 19 28,892,559 28,918,752 alt
GL456003.2 | NT_039739.2 129S6/SvEvTac Odz1 X 42,891,057 43,298,842 alt
GL456032.1 | NT_039744.2 129S1/SvImJ region57 X 72,166,181 72,363,206 alt
GL456004.1 | NT_099024.1 129S6/SvEvTac Xlr_region_1 X 73,003,651 73,121,964 alt
GL456033.2 | NT_039747.4 129S1/SvImJ Xlr_region_2 X 73,185,425 73,263,090 alt
GL456031.1 | NT_111920.1 129S1/SvImJ Xic X 103,589,284 103,841,870 alt
GL456071.1 | NT_166396.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456072.1 | NT_166398.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456073.1 | NT_166399.1 CAST/Ei unaligned Y not aligned not aligned alt
GL456080.1 | NT_166394.1 AKR/J unaligned Y not aligned not aligned alt
GL456081.1 | NT_166397.1 AKR/J unaligned Y not aligned not aligned alt
GL456082.1 | NT_166400.1 AKR/J unaligned Y not aligned not aligned alt
GL456050.1 | NT_080256.1 NOD/MrkTac unaligned Un not aligned not aligned alt

MGSCv37

  • Release date: September 23, 2010
  • 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 accessions: GenBank: GCA_000001635.1, RefSeq: GCF_000001635.18
Patches and alternate loci
Scaffold IDs Assembly unit Region name Chr Start Stop Type
GL456036.1 | NT_165757.1 NOD region1 1 60,697,653 61,195,514 alt
GL456038.1 | NT_039199.1 NOD region1 1 60,697,653 61,195,514 alt
GL456039.1 | NT_039200.1 NOD region1 1 60,697,653 61,195,514 alt
GL456037.1 | NT_039197.1 NOD region2 1 61,754,170 61,941,338 alt
GL456040.1 | NT_039201.1 NOD region3 1 63,440,029 63,634,836 alt
GL455993.1 | NT_039198.1 129/SvEvTac region4 1 78,410,334 78,684,064 alt
GL455991.1 | NT_039192.2 129/SvEvTac Ren2 1 135,135,713 135,386,019 alt
GL455992.1 | NT_039194.4 129/SvEvTac Ifi_cluster 1 175,631,261 175,981,314 alt
GL456005.1 | NT_039195.1 129/SvJ Ifi_cluster 1 175,631,261 175,981,314 alt
GL456024.1 | NT_039223.2 129/Sv region29 2 102,863,803 103,229,146 alt
GL456008.1 | NT_080257.1 129/SvJ unaligned 3 not aligned not aligned alt
GL456043.1 | NT_114258.1 NOD unaligned 3 not aligned not aligned alt
GL456050.1 | NT_080256.1 NOD unaligned 3 not aligned not aligned alt
GL456006.1 | NT_039248.1 129/SvJ region30 3 36,705,645 37,462,525 alt
GL456007.1 | NT_039256.1 129/SvJ region30 3 36,705,645 37,462,525 alt
GL456045.1 | NT_039247.1 NOD region30 3 36,705,645 37,462,525 alt
GL456048.1 | NT_039252.1 NOD region30 3 36,705,645 37,462,525 alt
GL456049.1 | NT_039257.3 NOD region31 3 47,250,927 47,483,886 alt
GL456041.1 | NT_109311.1 NOD region32 3 99,757,788 99,890,338 alt
GL456046.1 | NT_039250.1 NOD region33 3 100,124,682 100,629,140 alt
GL456047.1 | NT_039251.2 NOD region34 3 100,709,803 101,111,508 alt
GL456044.1 | NT_166287.1 NOD region35 3 103,394,301 103,719,496 alt
GL456042.1 | NT_114257.3 NOD region36 3 108,919,638 109,610,603 alt
GL455994.1 | NT_039291.1 129/SvEvTac unaligned 4 not aligned not aligned alt
GL456053.1 | NT_166299.1 NOD unaligned 4 not aligned not aligned alt
GL456077.1 | NT_166295.1 129S7/SvEv unaligned 4 not aligned not aligned alt
GL456010.1 | NT_039296.1 129/SvJ olfactory_region_2 4 43,775,564 43,869,886 alt
GL456075.1 | NT_166293.1 129S7/SvEv Mup_region_1 4 60,433,222 61,702,235 alt
GL456076.1 | NT_166294.1 129S7/SvEv Mup_region_2 4 61,706,289 61,898,563 alt
GL456064.1 | NT_039292.1 unknown strain region40 4 66,718,636 66,856,206 alt
GL456052.1 | NT_166298.1 NOD region41 4 129,222,696 129,387,052 alt
GL456051.1 | NT_166297.1 NOD region42 4 129,673,209 129,813,999 alt
GL456009.1 | NT_109318.2 129/SvJ Padi_cluster 4 140,277,012 140,517,363 alt
GL456011.1 | NT_109599.1 129/SvJ region44 5 91,082,154 91,255,787 alt
GL455995.1 | NT_039334.1 129/SvEvTac region45 5 151,674,830 151,925,798 alt
GL456025.1 | NT_039373.1 129/Sv region46 6 50,729,501 50,869,226 alt
GL456012.1 | NT_039372.1 129/SvJ region47 6 82,834,040 82,989,835 alt
GL456065.1 | NT_039367.1 unknown strain vomeronasal_region_1 6 90,040,061 90,240,457 alt
GL456026.1 | NT_039382.3 129/Sv region49 6 120,327,240 120,965,219 alt
GL456054.1 | NT_166305.1 NOD region50 6 144,953,971 145,181,710 alt
GL456014.1 | NT_078572.1 129/SvJ region51 7 28,528,234 28,611,868 alt
GL455989.1 | NT_095534.1 Balb/c Hbb_cluster 7 110,959,995 111,009,204 alt
GL456013.1 | NT_039443.1 129/SvJ olfactory_region_3 7 114,032,224 114,070,764 alt
GL455996.1 | NT_039469.1 129/SvEvTac region54 8 42,378,188 42,567,887 alt
GL455997.1 | NT_039470.1 129/SvEvTac Large 8 75,589,541 75,842,949 alt
GL456015.1 | NT_078651.1 129/SvJ Grm1 10 10,581,444 10,647,182 alt
GL456058.1 | NT_114883.1 NOD unaligned 11 not aligned not aligned alt
GL455998.1 | NT_078683.1 129/SvEvTac olfactory_region_1 11 58,426,683 58,600,787 alt
GL456055.1 | NT_110625.3 NOD region9 11 69,708,974 70,768,432 alt
GL456056.1 | NT_110626.2 NOD region9 11 69,708,974 70,768,432 alt
GL456059.1 | NT_165774.1 NOD region9 11 69,708,974 70,768,432 alt
GL456060.1 | NT_166317.1 NOD region10 11 72,722,413 72,881,612 alt
GL456057.1 | NT_114882.1 NOD region11 11 88,404,152 88,462,832 alt
GL456016.1 | NT_039525.1 129/SvJ Mapt 11 104,064,572 104,223,846 alt
GL456068.1 | NT_096355.1 unknown strain unaligned 12 not aligned not aligned alt
GL456074.1 | NT_114988.1 129/J unaligned 12 not aligned not aligned alt
GL456017.1 | NT_114985.2 129/SvJ Igh 12 105,978,478 115,696,908 alt
GL456018.1 | NT_039572.1 129/SvJ Igh 12 105,978,478 115,696,908 alt
GL456066.1 | NT_166319.1 unknown strain Igh 12 105,978,478 115,696,908 alt
GL456067.1 | NT_166320.1 unknown strain Igh 12 105,978,478 115,696,908 alt
GL456078.1 | NT_166322.1 129S7/SvEv Igh 12 105,978,478 115,696,908 alt
GL455990.1 | NT_039593.1 A/J Naip2_Naip5 13 100,922,006 101,021,810 alt
GL455999.1 | NT_039594.2 129/SvEvTac Ipo11 13 107,591,153 107,722,976 alt
GL456027.1 | NT_039613.3 129/Sv Fhit 14 11,148,176 11,650,860 alt
GL456020.1 | NT_096797.1 129/SvJ region17 14 52,482,687 52,593,237 alt
GL456019.1 | NT_039614.1 129/SvJ Tcra_Tcrd 14 52,971,974 54,848,751 alt
GL456000.1 | NT_039622.1 129/SvEvTac region19 15 80,333,302 80,502,798 alt
GL456028.1 | NT_039630.4 129/Sv DiGeorge 16 17,742,588 19,066,061 alt
GL456001.1 | NT_039634.3 129/SvEvTac DownSynCrit 16 94,114,517 95,701,295 alt
GL456029.1 | NT_039664.1 129/Sv unaligned 17 not aligned not aligned alt
GL456069.1 | NT_097336.1 unknown strain Airn 17 12,922,132 13,054,037 alt
GL456063.1 | NT_166329.1 NOD region23 17 27,450,268 27,705,657 alt
GL456061.1 | NT_165781.2 NOD region24 17 27,792,385 29,352,922 alt
GL456062.1 | NT_165782.2 NOD region24 17 27,792,385 29,352,922 alt
GL456022.1 | NT_039662.2 129/SvJ MHC_region_1 17 33,888,191 35,744,546 alt
GL456023.1 | NT_039663.1 129/SvJ MHC_region_1 17 33,888,191 35,744,546 alt
GL456002.1 | NT_039666.1 129/SvEvTac MHC_region_2 17 36,230,820 38,050,373 alt
GL456021.1 | NT_039661.3 129/SvJ MHC_region_2 17 36,230,820 38,050,373 alt
GL456030.1 | NT_039665.1 129/Sv MHC_region_2 17 36,230,820 38,050,373 alt
GL456070.1 | NT_165784.1 unknown strain Impact 18 11,308,623 11,423,912 alt
GL456079.1 | NT_039697.1 129P2/OlaHsd region28 19 5,679,043 5,707,799 alt
GL456003.1 | NT_039739.1 129/SvEvTac Odz1 X 40,330,809 40,652,019 alt
GL456032.1 | NT_039744.2 129/Sv region57 X 69,411,520 69,608,545 alt
GL456004.1 | NT_099024.1 129/SvEvTac Xlr_region_1 X 70,248,990 70,367,303 alt
GL456033.1 | NT_039747.3 129/Sv Xlr_region_2 X 70,430,764 70,508,135 alt
GL456031.1 | NT_111920.1 129/Sv Xic X 100,784,623 101,037,209 alt
GL456034.1 | NT_166393.1 Spret/Ei unaligned Y not aligned not aligned alt
GL456035.1 | NT_166395.1 Spret/Ei unaligned Y not aligned not aligned alt
GL456071.1 | NT_166396.1 Cast/Ei unaligned Y not aligned not aligned alt
GL456072.1 | NT_166398.1 Cast/Ei unaligned Y not aligned not aligned alt
GL456073.1 | NT_166399.1 Cast/Ei unaligned Y not aligned not aligned alt
GL456080.1 | NT_166394.1 AKR/J unaligned Y not aligned not aligned alt
GL456081.1 | NT_166397.1 AKR/J unaligned Y not aligned not aligned alt
GL456082.1 | NT_166400.1 AKR/J unaligned Y not aligned not aligned alt