Mouse assembly and gene annotation


This site features the latest major assembly release for mouse. The primary assembly, GRCm38, was released by the Genome Reference Consortium in January 2012. It is based on Mus musculus strain C57BL/6J. This assembly is used by UCSC to create their mm10 database.

The GRCm38 primary assembly comprises 21 chromosomes and 22 unplaced scaffolds. Similar to the human genome assembly, the Genome Reference Consortium will be releasing additional sequence for GRCm38 in the form of minor releases (patches).

To convert your old data from Mouse assembly m37 to m38, click on 'Manage your data' on any mouse page and select 'Assembly converter' from the left-hand menu.


As the GRC maintains and improves the mouse reference assembly, patches are being introduced. These patches do not change the coordinates of the primary assembly. For more information, please see our Genome Assemblies help document.

The genome assembly represented here corresponds to GenBank Assembly ID GCA_000001635.6

Other assemblies

Gene annotation

The mouse primary assembly GRCm38 was annotated using Ensembl's automatic annotation system. This includes an updated mouse-specific repeat library, RefSeq and Uniprot protein sequence data for annotating the coding regions of protein-coding genes, as well as mouse cDNAs and ESTs for annotation untranslated regions (UTRs) of protein-coding genes.

In current release, we continue to display a joint gene set based on the merge between the automatic annotation from Ensembl (May 2012) and the manually curated annotation from Havana. Transcripts from the two annotation sources were merged if they shared the same internal exon-intron boundaries (i.e. had identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Vega source transcripts (regardless of merge status) were included in the final merged gene set.

In addition to the gene set, we display alignments of mouse cDNA and EST sequences. The mouse cDNA alignments are updated for every Ensembl release. We also display alignments of sequences from UniProt, UniGene and the ENA vertebrate RNA collection, and ab initio gene predictions from Genscan. The Consensus Coding Sequence (CCDS) identifiers have also been mapped to the new assembly. More information about the CCDS project.

Vega logo Additional manual annotation of this genome can be found in Vega


Additional functional genomics data produced by the HEROIC project (High-throughput Epigenetic Regulatory Organisation In Chromatin) is available to download from the Ensembl Projects HEROIC portal.

More information

General information about this species can be found in Wikipedia.



AssemblyGRCm38.p4 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.6, Jan 2012
Database version81.38
Base Pairs3,482,010,803
Golden Path Length2,730,871,774
Genebuild byEnsembl
Genebuild methodFull genebuild
Genebuild startedJan 2012
Genebuild releasedJul 2012
Genebuild last updated/patchedJul 2015
Gencode versionGENCODE M6

Gene counts (Primary assembly)

Coding genes22,547 (incl 164 readthrough)
Non coding genes12,583
Small non coding genes5,530
Long non coding genes6,489 (incl 34 readthrough)
Misc non coding genes564
Pseudogenes8,770 (incl 4 readthrough)
Gene transcripts109,712

Gene counts (Alternative sequence)

Coding genes124
Non coding genes109
Small non coding genes74
Long non coding genes30
Misc non coding genes5


Genscan gene predictions56,984
Short Variants88,364,232
Structural variants791,899