#### README #### -------- GTF DUMP -------- This directory includes a summary of the gene annotation information and GTF format. Ensembl provides an automatic gene annotation for Oryza barthii. For some species ( human, mouse, zebrafish, pig and rat), the annotation provided through Ensembl also includes manual annotation from HAVANA. In the case of human and mouse, the GTF files found here are equivalent to the GENCODE gene set. GTF provides access to all annotated transcripts which make up an Ensembl gene set. Annotation is based on alignments of biological evidence (eg. proteins, cDNAs, RNA-seq) to a genome assembly. The annotation dumped here is transcribed and translated from the genome assembly and is not the original input sequence data that we used for alignment. Therefore, the sequences provided by Ensembl may differ from the original input sequence data where the genome assembly is different to the aligned sequence. Additionally, we provide a GTF file containing the predicted gene set as generated by Genscan and other abinitio prediction tools. This file is identified by the abinitio extension. ----------- FILE NAMES ------------ The files are consistently named following this pattern: ...gtf.gz : The systematic name of the species. : The assembly build name. : The version of Ensembl from which the data was exported. gtf : All files in these directories are in GTF format gz : All files are compacted with GNU Zip for storage efficiency. e.g. Homo_sapiens.GRCh38.81.gtf.gz For the predicted gene set, an additional abinitio flag is added to the name file. ...abinitio.gtf.gz e.g. Homo_sapiens.GRCh38.81.abinitio.gtf.gz -------------------------------- Definition and supported options -------------------------------- The GTF (General Transfer Format) is an extension of GFF version 2 and used to represent transcription models. GFF (General Feature Format) consists of one line per feature, each containing 9 columns of data. Fields 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. Pragmas/Metadata GTF files can contain meta-data. In the case of experimental meta-data these are noted by a #!. Those which are stable are noted by a ##. Meta data is a single key, a space and then the value. Current meta data keys are: * genome-build - Build identifier of the assembly e.g. GRCh37.p11 * genome-version - Version of this assembly e.g. GRCh37 * genome-date - The date of this assembly's release e.g. 2009-02 * genome-build-accession - The accession and source of this accession e.g. NCBI:GCA_000001405.14 * genebuild-last-updated - The date of the last genebuild update e.g. 2013-09 ------------------ Example GTF output ------------------ #!genome-build GRCh38 11 ensembl_havana gene 5422111 5423206 . + . gene_id "ENSG00000167360"; gene_version "4"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; 11 ensembl_havana transcript 5422111 5423206 . + . gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; 11 ensembl_havana exon 5422111 5423206 . + . gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; exon_number "1"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; exon_id "ENSE00001276439"; exon_version "4"; 11 ensembl_havana CDS 5422201 5423151 . + 0 gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; exon_number "1"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; protein_id "ENSP00000300778"; protein_version "4"; 11 ensembl_havana start_codon 5422201 5422203 . + 0 gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; exon_number "1"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; 11 ensembl_havana stop_codon 5423152 5423154 . + 0 gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; exon_number "1"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; 11 ensembl_havana UTR 5422111 5422200 . + . gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381"; 11 ensembl_havana UTR 5423155 5423206 . + . gene_id "ENSG00000167360"; gene_version "4"; transcript_id "ENST00000300778"; transcript_version "4"; gene_name "OR51Q1"; gene_source "ensembl_havana"; gene_biotype "protein_coding"; transcript_name "OR51Q1-001"; transcript_source "ensembl_havana"; transcript_biotype "protein_coding"; tag "CCDS"; ccds_id "CCDS31381";