Genomes Tables Help  
Mouse (Mus musculus) Genome Browser Gateway
The UCSC Genome Browser was created by the Genome Bioinformatics Group of UC Santa Cruz.
Software Copyright (c) The Regents of the University of California. All rights reserved.
clade genome assembly position or search term gene  

Click here to reset the browser user interface settings to their defaults.

About the Mouse July 2007 (NCBI37/mm9) assembly (sequences)
Mus musculus
(Photo courtesy of The Jackson Laboratory)

The July 2007 mouse (Mus musculus) genome data were obtained from the Build 37 assembly by NCBI and the Mouse Genome Sequencing Consortium. For more information about this assembly, see MGSCv37 in the NCBI Assembly database.

Sample position queries

A genome position can be specified by the accession number of a sequenced genomic region, an mRNA or EST, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA. The following list shows examples of valid 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 37, 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 Un (unmapped clone contigs). More information about this version is available on the NCBI Build 37 Data web page.

For information about the process used to assemble this version, see the NCBI website. 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. Note that the UCSC mm9 database contains only the reference strain C57BL/6J.

Bulk downloads of the sequence and annotation data are available via the Genome Browser FTP server or the Downloads page.

The mm9 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.

Genbank Pipeline Details

For the purposes of the Genbank alignment pipeline, this assembly is considered to be: finished.