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 the current release, we continue to display a joint gene set based on the merge between the automatic annotation from Ensembl and the manually curated annotation from Havana. See the statistics table, right, for the corresponding GENCODE version number. The Consensus Coding Sequence (CCDS) identifiers have also been mapped to the annotations. More information about the CCDS project.

Updated manual annotation from Havana is merged into the Ensembl annotation every release. Transcripts from the two annotation sources are merged if they share the same internal exon-intron boundaries (i.e. have identical splicing pattern) with slight differences in the terminal exons allowed. Importantly, all Havana transcripts are included in the final Ensembl/Havana merged (GENCODE) 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.

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 version82.38
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/patchedSep 2015
Gencode versionGENCODE M7

Gene counts (Primary assembly)

Coding genes22,528 (incl 179 readthrough)
Non coding genes12,775
Small non coding genes5,530
Long non coding genes6,681 (incl 40 readthrough)
Misc non coding genes564
Pseudogenes9,166 (incl 4 readthrough)
Gene transcripts111,801

Gene counts (Alternative sequence)

Coding genes145
Non coding genes114
Small non coding genes74
Long non coding genes35
Misc non coding genes5


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