Ensembl Mouse

Karyotype

Click on a chromosome for a closer view

About the Mouse genome

Assembly

Ensembl Mouse is based on the NCBI m37 mouse assembly (April 2007, strain C57BL/6J).

The Mouse Genome Sequencing Consortium is a joint project between The Whitehead Institute/MIT Center for Genome Research, The Washington University Genome Sequencing Center, The Wellcome Trust Sanger Institute and EMBL - EBI to provide the Mouse genome sequence to the world. We work closely with other Mouse groups to provide an integrated resource (see below for credits).

There are some major changes in the assembly from version m36; for more details see the NCBI build statistics .

Annotation

For release 47 the gene annotation presented has been a combined Ensembl-Havana geneset, which incorporates more than 15,000 full-length protein-coding transcripts annotated by the Havana team in addition to the Ensembl automatic gene build. The mouse genome sequence is now considered sufficiently stable that since September 2006 the major genome browsers have come together to produce a common set of identifiers where CDS annotations of transcripts can be agreed and these identifiers are also shown.

• More information about the CCDS project.

Modifications to the systems have further improved the gene set. 95% of the known genes and 47% of the novel genes from build m36 retain the same Ensembl gene ids in this release.

What's New in Ensembl 48

Mus musculus News

• Updated Mouse variation data
  The new dbSNP build 128 has been imported, and transcript_variation has been updated to reflect the Mouse patched gene set.
• Patched mouse data
  Ensembl Mus musculus has been patched by removing a number of bad genes/transcripts.
• cDNA updates
  Ensembl Human and Mouse have both had their regular cDNA updates in this release.
• Vega updates
  New Human and Mouse data has been released on VEGA.

General News

• Change to SliceAdaptor
  The method fetch_by_region() in Bio::EnsEMBL::DBSQL::SliceAdaptor has an additional optional argument $no_fuzz which, if set to a true value, will ensure that the fuzzy matching is not performed when no exact match for the given $seq_region_name is found.
  Read more...

More news...

Links

• Mouse sequencing project credits
• Additional mouse resources
• The mouse physical map has been published in Nature

Statistics

* Total number of base pairs = sum of lengths of DNA table

** Reference assembly (Golden path) length = sum of non-redundant top level seq regions