Release M33 (GRCm39)

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