Mus musculus (Photo courtesy of The Jackson Laboratory)

The May 2004 mouse (Mus musculus) draft genome data was obtained from the Build 33 assembly by NCBI.

### 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
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

This assembly is a composite version in which phase 3 High Throughput Genome Sequence (HTGS) was merged with the Mouse Genome Sequencing Consortium v3 Whole Genome Shotgun Assembly (MGSCv3). The assembly was performed by NCBI using a "combined" tiling path that was created automatically for the most part, but was manually curated in places. This facilitated the placement of finished sequence in the context of the MGSCv3 assembly. Draft sequence was not included in this build: the slight increase in coverage gained by using this would have been offset by the increase in build errors. The UCSC mm5 assembly contains only the reference strain C57BL/6J.

Build 33 includes approximately 2.6 gigabases of sequence contained in chromosomes 1-19, X, Y, M (mitochondrial DNA) and Un (unmapped clone contigs). Chromosome 11 is finished in this assembly; the Sanger Institute has provided the corresponding agp file. The whole genome N50 for Build 33 is 22.3 Mb, in comparison to 17.7 Mb for the previous build. More information about this version is available in the NCBI assembly notes and Build 33 statistics.

The mm5 sequence and annotation data may be downloaded from the Genome Browser FTP server or Downloads web page. The mm5 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.