GTF-Format

Fields of the GTF format

Fields are tab-separated. Also, all but the final field in each feature line must contain a value; “empty” columns are denoted with a ‘.’

seqname   - name of the chromosome or scaffold; chromosome names 
            without a 'chr' 
source    - name of the program that generated this feature, or 
            the data source (database or project name)
feature   - feature type name. Current allowed features are
            {gene, transcript, exon, CDS, Selenocysteine, start_codon,
            stop_codon and UTR}
start     - start position of the feature, with sequence numbering 
            starting at 1.
end       - end position of the feature, with sequence numbering 
            starting at 1.
score     - a floating point value indiciating the score of a feature
strand    - defined as + (forward) or - (reverse).
frame     - one of '0', '1' or '2'. Frame indicates the number of base pairs
            before you encounter a full codon. '0' indicates the feature 
            begins with a whole codon. '1' indicates there is an extra
            base (the 3rd base of the prior codon) at the start of this feature.
            '2' indicates there are two extra bases (2nd and 3rd base of the 
            prior exon) before the first codon. All values are given with
            relation to the 5' end.
attribute - a semicolon-separated list of tag-value pairs (separated by a space), 
            providing additional information about each feature. A key can be
            repeated multiple times.

Attributes

The following attributes are available. All attributes are semi-colon separated pairs of keys and values.

  • gene_id: The stable identifier for the gene
  • gene_version: The stable identifier version for the gene
  • gene_name: The official symbol of this gene
  • gene_source: The annotation source for this gene
  • gene_biotype: The biotype of this gene
  • transcript_id: The stable identifier for this transcript
  • transcript_version: The stable identifier version for this transcript
  • transcript_name: The symbold for this transcript derived from the gene name
  • transcript_source: The annotation source for this transcript
  • transcript_biotype: The biotype for this transcript
  • exon_id: The stable identifier for this exon
  • exon_version: The stable identifier version for this exon
  • exon_number: Position of this exon in the transcript
  • ccds_id: CCDS identifier linked to this transcript
  • protein_id: Stable identifier for this transcript’s protein
  • protein_version: Stable identifier version for this transcript’s protein
  • tag: A collection of additional key value tags
  • transcript_support_level: Ranking to assess how well a transcript is supported (from 1 to 5)

Tags

Tags are additional flags used to indicate attibutes of the transcript.

  • CCDS: Flags this transcript as one linked to a CCDS record
  • seleno: Flags this transcript has a Selenocysteine edit. Look for the Selenocysteine feature for the position of this on the genome
  • cds_end_NF: the coding region end could not be confirmed
  • cds_start_NF: the coding region start could not be confirmed
  • mRNA_end_NF: the mRNA end could not be confirmed
  • mRNA_start_NF: the mRNA start could not be confirmed.
  • basic: the transcript is part of the gencode basic geneset

Comments

Lines may be commented out by the addition of a single # character at the start. These lines should be ignored by your parser.