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.
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. |