Mus musculus
(Photo courtesy of The Jackson Laboratory)

The August 2005 mouse (Mus musculus) draft genome data was obtained from the Build 35 assembly by NCBI. See the Assembly Details section below for information about the differences between Build 35 and Build 35.1.

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.

  Genome Browser Response:

chr16   Displays all of chromosome 16
chr16:1-5000000   Displays first 5 million bases of chr 16
chr16:1000000+2000 Displays a region of chr 16 that spans 2000 bases, starting with position 1000000
AC072048.4   Displays region of contig AC072048.4
D16Mit120   Displays region around STS marker DMit16120 from the MGI consensus genetic map, including 100,000 bases on each side as well
D16Mit120;D16Mit149   Displays region between STS markers D16Mit120 and D16Mit149

BC012683   Displays alignment location of mRNA with GenBank accession BC012683
AW045217   Displays alignment location 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
Smith,D.   Lists mRNAs deposited by co-author D. Smith

Use this last format for author queries. Although GenBank requires the search format Smith D, internally it uses the format Smith,D..

Assembly Details

NCBI Build 35 includes approximately 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence, contained in chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). Chromosomes 2, 4, 11 and X are finished in this assembly. More information about this version is available on the NCBI Build 35 Data web page.

Build 35 is a fifth-generation composite assembly. In this build, chromosomes 1,3,5,6,7,8,9,10, and 12-19 were automatically assembled. The assembly is made up of high throughput genome sequence (HTGS) phase 3 contigs, single fragment HTGS phase 2 contigs and whole genome shotgun (WGS) contigs. On chromosome Y in this assembly, only the short arm has reliable mapping data; therefore, most of the contigs on the Y chromosome are unplaced. For more information about the assembly process, see the NCBI website.

Notes on the UCSC mm7 version:

- The UCSC mm7 database contains only the reference strain C57BL/6J.

- The Build 35 assembly has a known problem: five contigs were erroneously placed at the end of chromosome 5 (Mm5_160001_35, Mm5_160002_35, Mm5_160003_35, Mm5_160004_35, and Mm5_160005_35). Because the UCSC mm7 data are derived from Build 35, this problem is also present in the UCSC browser, which incorrectly extends the length of chr5 by approximately 3,000,000 bp. NCBI has subsequently released Build 35.1, which corrects this problem. Due to the effort involved, UCSC does not plan to upgrade the mm7 browser to the Build 35.1 assembly.

The mm7 sequence and annotation data can be downloaded from the Genome Browser FTP server or Downloads web page. The mm7 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 this release.