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.
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.
General information about this species can be found in Wikipedia.
|Assembly||GRCm38.p6 (Genome Reference Consortium Mouse Reference 38), INSDC Assembly GCA_000001635.8, Jan 2012|
|Golden Path Length||2,730,871,774|
|Annotation method||Full genebuild|
|Genebuild started||Jan 2012|
|Genebuild released||Jul 2012|
|Genebuild last updated/patched||Feb 2020|
|Gencode version||GENCODE M25|
Gene counts (Primary assembly)
|Coding genes||22,519 (incl 273 ) readthrough|
|Non coding genes||16,074|
|Small non coding genes||5,531|
|Long non coding genes||9,981 (incl 75 ) readthrough|
|Misc non coding genes||562|
|Pseudogenes||13,656 (incl 4 ) readthrough|
Gene counts (Alternative sequence)
|Coding genes||351 (incl 5 ) readthrough|
|Non coding genes||227|
|Small non coding genes||110|
|Long non coding genes||111 (incl 1 ) readthrough|
|Misc non coding genes||6|
|Genscan gene predictions||57,381|