The Mouse Genomes Project

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The Mouse Genomes Project is an ongoing effort to catalog all forms of genetic variation between the common laboratory mouse strains and to produce high quality annotated reference genomes for the key strains.

Ensembl genome annotation was generated by mapping GENCODE M30 genes and transcripts via the Ensembl Human automated annotation system, supplemented by methods from the Ensembl vertebrate annotation pipeline. Mapped GENCODE structures served as the primary evidence with gaps in the annotations filled using aligned short-read transcriptomic data and full-length transcripts derived from PacBio IsoSeq long-read data.

Species	Strain	Accession	Annotation	Proteins	Transcripts	Softmasked genome	Other data	View in browser
Mus musculus	Reference	GCA_000001635.9	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	beta.ensembl.org
Mus musculus	C57BL_6J (T2T)	GCA_964188535.1	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	beta.ensembl.org
Mus musculus castaneus	CAST_EiJ (T2T)	GCA_964188545.1	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	beta.ensembl.org
Mus musculus	C57BL_6NJ	GCA_921999865.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	NZO_HlLtJ	GCA_947593165.1	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	BALB_cJ	GCA_921997145.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	FVB_NJ	GCA_921998635.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	129S1_SvImJ	GCA_921998555.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	C3H_HeJ	GCA_921997125.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	AKR_J	GCA_922000895.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	DBA_2J	GCA_921998315.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	A_J	GCA_921998355.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	LP_J	GCA_947599735.1	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	NOD_ShiLtJ	GCA_921998325.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus	CBA_J	GCA_921998905.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus castaneus	CAST_EiJ	GCA_921999005.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus domesticus	WSB_EiJ	GCA_921998345.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus molossinus	JF1_MsJ	GCA_921999095.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org
Mus musculus musculus	PWK_PhJ	GCA_921998335.2	GTF, GFF3	FASTA	FASTA	FASTA	FTP dumps	rapid.ensembl.org