Mus musculus (Photo courtesy of The Jackson Laboratory)

UCSC Genome Browser assembly ID: mm10
Sequencing/Assembly provider ID: Genome Reference Consortium Mouse Build 38 (GCA_000001635.2)
Assembly date: Dec. 2011
Accession ID: GCA_000001305.2
NCBI Genome ID: 52 (Mus musculus)
NCBI Assembly ID: 327618 (GRCm38/GCA_000001635.2)
NCBI BioProject ID: 20689

Other mice strains are available here.

Search the assembly:

• By position or search term: Use the "position or search term" box to find areas of the genome associated with many different attributes, such as a specific chromosomal coordinate range; mRNA, EST, or STS marker names; or keywords from the GenBank description of an mRNA. More information, including sample queries.
• By gene name: Type a gene name into the "search term" box, choose your gene from the drop-down list, then press "submit" to go directly to the assembly location associated with that gene. More information.
• By track type: Click the "track search" button to find Genome Browser tracks that match specific selection criteria. More information.

Download sequence and annotation data:

• Using rsync (recommended)
• Using FTP
• Using HTTP
• Data use conditions and restrictions
• Acknowledgments

Assembly details

Genome Reference Consortium GRCm38, which includes approximately 2.6 Gb of sequence, is considered to be "essentially complete". The assembly includes chromosomes 1-19, X, Y, M (mitochondrial DNA) and chr*_random (unlocalized) and chrUn_* (unplaced clone contigs). For information about the process used to assemble this version, see the GRC website. For a glossary of assembly-related terms, see the GRC Assembly Terminology page.

mm10 has been updated with patches since its release in 2012. GRC patch releases do not change any previously existing sequences; they simply add new sequences for fix patches or alternate haplotypes that correspond to specific regions of the main chromosome sequences. For most users, the patches are unlikely to make a difference and may complicate the analysis as they introduce more duplication.

The UCSC mm10 patch level 6 contains 9 alternate scaoffolds from the reference strain C57BL/6J.

• chr1_KK082441_alt
• chr11_KZ289080_alt
• chr11_KZ289074_alt
• chr11_KZ289078_alt
• chr11_KZ289081_alt
• chr11_KZ289079_alt
• chr11_KZ289075_alt
• chr11_KZ289073_alt
• chr11_KZ289077_alt

It also contains 99 alternate scaffolds from 14 other mouse strains which are included in the NCBI release GRC MM38.

Other Mouse Strains:

• 129P2/OlaHsd
• 129S1/SvImJ
• 129S2/SvPas
• 129S6/SvEvTac
• 129X1/SvJ
• A/J
• AKR/J
• BALB/c
• CAST/Ei
• NOD/MrkTac
• NOD/ShiLtJ
• RIII
• UNKNOWN
• 129S7/SvEvBrd-Hprt-b-m2