Release M33 (GRCm39)

Statistics of this release
More information about this assembly (including patches, scaffolds and haplotypes)

GTF / GFF3 files

Content	Regions	Description	Download
Comprehensive gene annotation	CHR	It contains the comprehensive gene annotation on the reference chromosomes only	GTF GFF3
Comprehensive gene annotation	ALL	It contains the comprehensive gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes)	GTF GFF3
Comprehensive gene annotation	PRI	It contains the comprehensive gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions	GTF GFF3
Basic gene annotation	CHR	It contains the basic gene annotation on the reference chromosomes only This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene This is the main annotation file for most users	GTF GFF3
Basic gene annotation	ALL	It contains the basic gene annotation on the reference chromosomes, scaffolds, assembly patches and alternate loci (haplotypes) This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene This is a superset of the main annotation file	GTF GFF3
Basic gene annotation	PRI	It contains the basic gene annotation on the primary assembly (chromosomes and scaffolds) sequence regions This is a subset of the corresponding comprehensive annotation, including only those transcripts tagged as 'basic' in every gene	GTF GFF3
Long non-coding RNA gene annotation	CHR	It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes	GTF GFF3
PolyA feature annotation	CHR	It contains the polyA features (polyA_signal, polyA_site, pseudo_polyA) manually annotated by HAVANA on the reference chromosomes This dataset does not form part of the main annotation file	GTF GFF3
Consensus pseudogenes predicted by the Yale and UCSC pipelines	CHR	2-way consensus (retrotransposed) pseudogenes predicted by the Yale and UCSC pipelines, but not by HAVANA, on the reference chromosomes This dataset does not form part of the main annotation file	GTF GFF3
Predicted tRNA genes	CHR	tRNA genes predicted by ENSEMBL on the reference chromosomes using tRNAscan-SE This dataset does not form part of the main annotation file	GTF GFF3

Fasta files

Content	Regions	Description	Download
Transcript sequences	CHR	Nucleotide sequences of all transcripts on the reference chromosomes	Fasta
Protein-coding transcript sequences	CHR	Nucleotide sequences of coding transcripts on the reference chromosomes Transcript biotypes: protein_coding, nonsense_mediated_decay, non_stop_decay, IG__gene, TR__gene, polymorphic_pseudogene, protein_coding_LoF	Fasta
Protein-coding transcript translation sequences	CHR	Amino acid sequences of coding transcript translations on the reference chromosomes Transcript biotypes: protein_coding, nonsense_mediated_decay, non_stop_decay, IG__gene, TR__gene, polymorphic_pseudogene, protein_coding_LoF	Fasta
Long non-coding RNA transcript sequences	CHR	Nucleotide sequences of long non-coding RNA transcripts on the reference chromosomes	Fasta
Genome sequence (GRCm39)	ALL	Nucleotide sequence of the GRCm39 genome assembly version on all regions, including reference chromosomes, scaffolds, assembly patches and haplotypes The sequence region names are the same as in the GTF/GFF3 files	Fasta
Genome sequence, primary assembly (GRCm39)	PRI	Nucleotide sequence of the GRCm39 primary genome assembly (chromosomes and scaffolds) The sequence region names are the same as in the GTF/GFF3 files	Fasta

Metadata files

Content	Regions	Description	Download
Annotation remarks	ALL	Remarks made during the manual annotation of the transcript	Metadata
Entrez gene ids	ALL	Entrez gene ids associated to GENCODE transcripts (from Ensembl xref pipeline)	Metadata
Exon annotation evidence	ALL	Piece of evidence used in the annotation of an exon (usually peptides, mRNAs, ESTs)	Metadata
Gene source	ALL	Source of the gene annotation (Ensembl, Havana, Ensembl-Havana merged model or imported in the case of small RNA and mitochondrial genes)	Metadata
Gene symbol	ALL	MGI approved gene symbol (from Ensembl xref pipeline)	Metadata
PDB id	ALL	PDB entries associated to the transcript (from Ensembl xref pipeline)	Metadata
PolyA features	ALL	Manually annotated polyA features overlapping the transcript 3'-end	Metadata
PubMed id	ALL	Pubmed ids of publications associated to the transcript (from MGI website)	Metadata
RefSeq	ALL	RefSeq RNA and/or protein associated to the transcript (from Ensembl xref pipeline)	Metadata
Selenocysteine	ALL	Amino acid position of a selenocysteine residue in the transcript	Metadata
SwissProt	ALL	UniProtKB/SwissProt entry associated to the transcript (from Ensembl xref pipeline)	Metadata
Transcript source	ALL	Source of the transcript annotation	Metadata
Transcript annotation evidence	ALL	Piece of evidence used in the annotation of the transcript	Metadata
TrEMBL	ALL	UniProtKB/TrEMBL entry associated to the transcript (from Ensembl xref pipeline)	Metadata