Mouse strains

Assembly and annotation

The Mouse Genomes Project is an ongoing effort to sequence the genomes of the common laboratory mouse strains, cataloguing all forms of molecular variation. They have produced de novo assemblies and strain-specific gene annotation for 16 laboratory and wild-derived strains (129S1/SvImJ, A/J, ARK/J, BALB/cJ, C3H/HeJ, C57BL/6NJ, CAST/EiJ, CBA/J, DBA/2J, FVB/NJ, LP/J, NOD/ShiLtJ, NZO/HlLtJ, PWK/PhJ, SPRET/EiJ, and WSB/EiJ) from a mixture of short- and long-range illumina libraries, optical maps, and third generation sequencing.

The strain-specific genome annotation was created by a combination of mapping over Gencode M8 mouse transcripts, strain-specific RNA-seq to refine mapped transcripts with Augustus, and Augustus CGP (comparative gene prediction) with strain-specific RNA-seq to annotate novel or private transcripts.

The assemblies and annotation were loaded into the Ensembl framework and additional analyses were run. These included: repeatmasking using Repeatmasker; ab initio gene predictions from Genscan; CpG island identification; prediction of transcription start sites using Eponine; tRNA predictions from tRNAscan; alignments of sequences from UniProt, UniGene and the ENA vertebrate RNA collection. Protein domains were annotated using InterProScan.

Comparative analysis

The Mouse Genomes Project has provided a multiple alignment of all their genomes with Mus musculus and Rattus norvegicus in the form of a HAL file generated by the progressive-Cactus aligner. Additionally, we have computed a LastZ alignment of human and Mus spretus.

We provide two sets of gene-trees and orthologues in Ensembl. The standard gene-trees and orthologues comprise genes from one representative for every Ensembl species, whilst the Murinae-specific gene-trees and orthologues comprise genes from all mouse strains and include genes from Mus musculus, Mus spretus and Rattus norvegicus. A stepwise approach via one these three species is required in order to compare genes from mouse strains to genes from species not in the Murinae set.

StrainScientific nameEnsembl AssemblyAccessionMore information
iconMouse 129S1/SvImJ
View example location | Karyotype and statistics
Mus musculus129S1_SvImJ_v1GCA_001624185.1Strain datasheet (Jackson Labs)
iconMouse A/J
View example location | Karyotype and statistics
Mus musculusA_J_v1GCA_001624215.1Strain datasheet (Jackson Labs)
iconMouse AKR/J
View example location | Karyotype and statistics
Mus musculusAKR_J_v1GCA_001624295.1Strain datasheet (Jackson Labs)
iconMouse BALB/cJ
View example location | Karyotype and statistics
Mus musculusBALB_cJ_v1GCA_001632525.1Strain datasheet (Jackson Labs)
iconMouse C3H/HeJ
View example location | Karyotype and statistics
Mus musculusC3H_HeJ_v1GCA_001632575.1Strain datasheet (Jackson Labs)
iconMouse C57BL/6NJ
View example location | Karyotype and statistics
Mus musculusC57BL_6NJ_v1GCA_001632555.1Strain datasheet (Jackson Labs)
iconMouse CAST/EiJ
View example location | Karyotype and statistics
Mus musculus castaneusCAST_EiJ_v1GCA_001624445.1Strain datasheet (Jackson Labs)
iconMouse CBA/J
View example location | Karyotype and statistics
Mus musculusCBA_J_v1GCA_001624475.1Strain datasheet (Jackson Labs)
iconMouse DBA/2J
View example location | Karyotype and statistics
Mus musculusDBA_2J_v1GCA_001624505.1Strain datasheet (Jackson Labs)
iconMouse FVB/NJ
View example location | Karyotype and statistics
Mus musculusFVB_NJ_v1GCA_001624535.1Strain datasheet (Jackson Labs)
iconMouse LP/J
View example location | Karyotype and statistics
Mus musculusLP_J_v1GCA_001632615.1Strain datasheet (Jackson Labs)
iconMouse NOD/ShiLtJ
View example location | Karyotype and statistics
Mus musculusNOD_ShiLtJ_v1GCA_001624675.1Strain datasheet (Jackson Labs)
iconMouse NZO/HlLtJ
View example location | Karyotype and statistics
Mus musculusNZO_HlLtJ_v1GCA_001624745.1Strain datasheet (Jackson Labs)
iconMouse PWK/PhJ
View example location | Karyotype and statistics
Mus musculus musculusPWK_PhJ_v1GCA_001624775.1Strain datasheet (Jackson Labs)
iconMouse WSB/EiJ
View example location | Karyotype and statistics
Mus musculus domesticusWSB_EiJ_v1GCA_001624835.1Strain datasheet (Jackson Labs)
iconMouse SPRET/EiJ
View example location | Karyotype and statistics
Mus spretusSPRET_EiJ_v1GCA_001624865.1Strain datasheet (Jackson Labs)

About this species