About the Mus musculus assembly

The latest mouse genome assembly (UCSC version mm4) is based on NCBI Build 32, a composite assembly of MGSCv3 produced by the Mouse Genome Sequencing Consortium and finished BAC sequence. There is a slight difference between the UCSC and NCBI versions: the NCBI assembly includes contigs from several strains, but the UCSC version contains only the reference strain (C57BL/6J). The current assembly includes 705 megabases of finished sequence. While there are many gaps in the sequence, the order and orientation of the contigs on either side of a gap are known in almost all cases. We estimate that 90-96 percent of the mouse genome is present in the assembly.

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 Guide for more help.

Request:
   Genome Browser Response:

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

D16Mit120 Displays region around STS marker DMit16120 from the MGI consensus genetic map. Includes 100,000 bases on each side as well.
D16Mit203;D16Mit70 Displays region between STS markers D16Mit203 and D16Mit70. Includes 100,000 bases on each side as well.
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
Lists candidate genes associated with Huntington's disease
Evans,J.E. Lists mRNAs deposited by co-author J.E. Evans

Use this last format for entry authors -- even though Genbank searches require Evans JE format, GenBank entries themselves use Evans,J.E. internally.