Mouse
Mus musculus
 (Photo courtesy of The Jackson Laboratory)

The October 2003 mouse (Mus musculus) genome assembly is based on NCBI Build 32.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic clone, an mRNA or EST or STS marker, or a cytological band, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list provides examples of various types of position queries for the mouse genome. See the User's Guide for more information.

Request:
    Genome Browser Response:

chr16   Displays all of chromosome 16
chr16:1-5000000   Displays first 5 million bases of chr 16

AW045217   Displays region of EST with GenBank accession AW045217
Ncam2   Displays region of genome with official MGI mouse genetic nomenclature Ncam2

pseudogene mRNA   Lists transcribed pseudogenes but not cDNAs
zinc finger   Lists many zinc finger mRNAs
kruppel zinc finger   Lists only kruppel-like zinc fingers
huntington   Lists candidate genes associated with Huntington's disease
Xu,C.S.   Lists mRNAs deposited by co-author C.S. Xu

Use this last format for author queries. Although GenBank requires the search format Xu CS, internally it uses the format Xu,C.S..

Assembly details

This assembly is a composite version in which chromosomes were assembled by two slightly different algorithms depending on the available mapping data. Chromosomes 2, 4, 5, 7, 11, 15, 18, 19, X, and Y were assembled using a clone-based tiling path file (TPF) provided by the Mouse Genome Sequencing Consortium (MGSC), with whole genome shotgun sequence used to fill gaps when necessary. The remaining chromosomes were assembled using the MGSCv3 whole genome shotgun assembly as the TPF and merging High Throughput Genomic Sequence (HTGS) as needed. The UCSC mm4 assembly contains only the reference strain C57BL/6J.

Build 32 includes 2.6 gigabases of sequence — 1.2 Gb of which is finished — contained in chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). We estimate that 90-96 percent of the mouse genome is present in the assembly. For more information about this version, see the NCBI assembly notes and Build 32 statistics. For an analysis of some problems found with this assembly, see the Ensembl Mus musculus web page.

The mm4 sequence and annotation data may be downloaded from the UCSC Genome Browser FTP server or Downloads web page. The mm4 annotation tracks were generated by UCSC and collaborators worldwide. See the credits page for a detailed list of the organizations and individuals who contributed to the success of this release.