Human

Release 39 (GRCh37)

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 originally created on the GRCh38 reference chromosomes, mapped to the GRCh37 primary assembly with gencode-backmap This is the main annotation file for most users Note that automated annotation ('ENSEMBL') was not mapped to GRCh37 in this release. The corresponding annotation was obtained from GENCODE 19 Also note that some manually annotated ('HAVANA') genes did not map properly to GRCh37. Their annotation was copied from GENCODE 19 if available, or they are completely absent otherwise. The gene annotation mapping summary can be found here	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	GTF GFF3
Long non-coding RNA gene annotation	CHR	It contains the comprehensive gene annotation of lncRNA genes on the reference chromosomes This is a subset 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	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	Fasta
Long non-coding RNA transcript sequences	CHR	Nucleotide sequences of long non-coding RNA transcripts on the reference chromosomes	Fasta
Genome sequence, primary assembly (GRCh37)	PRI	Nucleotide sequence of the GRCh37 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	CHR	Remarks made during the manual annotation of the transcript	Metadata
Entrez gene ids	CHR	Entrez gene ids associated to GENCODE transcripts (from Ensembl xref pipeline)	Metadata
Gene source	CHR	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	CHR	HGNC approved gene symbol (from Ensembl xref pipeline)	Metadata
PDB id	CHR	PDB entries associated to the transcript (from Ensembl xref pipeline)	Metadata
PubMed id	CHR	Pubmed ids of publications associated to the transcript (from HGNC website)	Metadata
RefSeq	CHR	RefSeq RNA and/or protein associated to the transcript (from Ensembl xref pipeline)	Metadata
SwissProt	CHR	UniProtKB/SwissProt entry associated to the transcript (from Ensembl xref pipeline)	Metadata
Transcript source	CHR	Source of the transcript annotation	Metadata
Transcript annotation evidence	CHR	Piece of evidence used in the annotation of the transcript	Metadata
TrEMBL	CHR	UniProtKB/TrEMBL entry associated to the transcript (from Ensembl xref pipeline)	Metadata