GRC logo Genome Reference Consortium
Skip navigation and go to main content

Mouse Genome Overview

Information concerning the continuing improvement of the mouse genome

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

Next assembly update

The next assembly update (patch release 4) will be a minor update (only patches) and is planned for late 2014..

Loading ideogram...

An ideogram representation of the latest mouse assembly, GRCm38.p3 (not showing unplaced or unlocalized sequences).

GRCm38.p3

  • Release date: March 22, 2014
  • Release type: minor
  • Release notes: Minor update of the assembly. No chromosome coordinate changes were made. There are 3 new patches with this update (2 FIX and 1 NOVEL) and 1 updated FIX patch.
  • Assembly accession: GCF_000001635.23
  • Pseudoautosomal region information for GRCm38.p3
    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 for GRCm38.p3
    Sequence 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
    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
    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
    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
    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
    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 6 129,636,567 130,660,308 alt
    KK082443.1 | NW_006763130.1 PATCHES NOD_mouse_Idd6.3 6 129,636,567 130,660,308 fix
    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
    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
    KB469738.2 | NW_004450259.2 PATCHES Nlrp4g 9 124,268,539 124,479,149 fix
    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
    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
    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
    KB469741.1 | NW_004450262.1 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
    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
    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
    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
    JH584319.1 | NT_187018.1 UNKNOWN Slc1a1 19 28,892,559 28,918,752 alt
    GL456050.1 | NT_080256.1 NOD/MrkTac unaligned Un not aligned not aligned alt
    JH792831.1 | NW_004058055.1 PATCHES region77 X 37,804,742 37,986,547 fix
    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
    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
    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

GRCm38

MGSCv37

Page last updated: March 18, 2013