Ensembl mobile site help

Things to know when navigating the Ensembl mobile site

Search box

Use the search box at the top right of all Ensembl views to search for a gene, phenotype, sequence variant, and more.

Top navigation

Touch MENU button to open the main menu and touch again to close.

Touch MENU

Left hand side menu

Touch the left menu icon () or swipe right to open the side menu and touch anywhere outside the menu or touch the cross icon or swipe left to close.

The ? icon

Touch the icon to get help

And don't forget to send us your comments using the feedback link inside the main menu.

EnsemblEnsembl Home

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.



AssemblyGRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012
Base Pairs3,486,944,526
Golden Path Length2,730,871,774
Annotation providerEnsembl
Annotation methodFull genebuild
Genebuild startedJan 2012
Genebuild releasedJul 2012
Genebuild last updated/patchedFeb 2020
Database version101.38
Gencode versionGENCODE M25

Gene counts (Primary assembly)

Coding genes22,519 (incl 273 readthrough)
Non coding genes16,074
Small non coding genes5,531
Long non coding genes9,981 (incl 75 readthrough)
Misc non coding genes562
Pseudogenes13,656 (incl 4 readthrough)
Gene transcripts142,699

Gene counts (Alternative sequence)

Coding genes351 (incl 5 readthrough)
Non coding genes227
Small non coding genes110
Long non coding genes111 (incl 1 readthrough)
Misc non coding genes6
Gene transcripts2,027


Genscan gene predictions57,381
Short Variants83,761,978
Structural variants791,878

About this species