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

As of 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.

Additional manual annotation of this genome can be found in Vega