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Mouse assembly and gene annotation

The house mouse (Mus musculus) is a small mammal of the order Rodentia, characteristically having a pointed snout, small rounded ears, and a long naked or almost hairless tail. It is one of the most abundant species of the genus Mus. Although a wild animal, the house mouse mainly lives in association with humans.The house mouse has been domesticated as the pet or fancy mouse, and as the laboratory mouse, which is one of the most important model organisms in biology and medicine.


The GRCm38.p6 assembly was submitted by Genome Reference Consortium on September 2017. The assembly is on chromosome level, consisting of 885 contigs assembled into 336 scaffolds. From these sequences, 21 chromosomes have been built. The N50 size is the length such that 50% of the assembled genome lies in blocks of the N50 size or longer. The N50 length for the contigs is 32,273,079 while the scaffold N50 is 52,589,046.

Gene annotation

The gene annotation process was carried out using a combination of protein-to-genome alignments, annotation mapping from a suitable reference species and RNA-seq alignments (where RNA-seq data with appropriate meta data were publicly available). For each candidate gene region, a selection process was applied to choose the most appropriate set of transcripts based on evolutionary distance, experimental evidence for the source data and quality of the alignments.
Small ncRNAs were obtained using a combination of BLAST and Infernal/RNAfold.
Pseudogenes were calculated by looking at genes with a large percentage of non-biological introns (introns of <10bp), where the gene was covered in repeats, or where the gene was single exon and evidence of a functional multi-exon paralog was found elsewhere in the genome.
lincRNAs were generated via RNA-seq data where no evidence of protein homology or protein domains could be found in the transcript.

In accordance with the Fort Lauderdale Agreement, please check the publication status of the genome/assembly before publishing any genome-wide analyses using these data.

More information

General information about this species can be found in Wikipedia.



AssemblyGRCm39 (Genome Reference Consortium Mouse Reference 39), INSDC Assembly GCA_000001635.9, Jun 2020
Base Pairs2,728,222,451
Golden Path Length2,728,222,451
Assembly providerGenome Reference Consortium
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedAug 2020
Genebuild released
Genebuild last updated/patchedMar 2021
Database version104.39
Gencode versionGENCODE M27

Gene counts

Coding genes22,468 (incl 253 readthrough)
Non coding genes16,060
Small non coding genes5,526
Long non coding genes9,972 (incl 76 readthrough)
Misc non coding genes562
Pseudogenes13,650 (incl 1 readthrough)
Gene transcripts142,434


Short Variants83,318,087
Structural variants791,878

About this species