#### README ####
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GFF FLATFILE DUMPS
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Gene annotation is provided in GFF3 format. Detailed specification of
the format is maintained by the Sequence Ontology:
https://github.com/The-Sequence-Ontology/Specifications/blob/master/gff3.md
GFF3 files are validated using GenomeTools: http://genometools.org
For chromosomal assemblies, in addition to a file containing all
genes, there are per-chromosome files. If a predicted geneset is
available (generated by Genscan and other ab initio tools), these
genes are in a separate 'abinitio' file.
The 'type' of gene features is:
* "gene" for protein-coding genes
* "ncRNA_gene" for RNA genes
* "pseudogene" for pseudogenes
The 'type' of transcript features is:
* "mRNA" for protein-coding transcripts
* a specific type or RNA transcript such as "snoRNA" or "lnc_RNA"
* "pseudogenic_transcript" for pseudogenes
All transcripts are linked to "exon" features.
Protein-coding transcripts are linked to "CDS", "five_prime_UTR", and
"three_prime_UTR" features.
Attributes for feature types:
(square brackets indicate data which is not available for all features)
* region types:
* ID: Unique identifier, format "<region_type>:<region_name>"
* [Alias]: A comma-separated list of aliases, usually including the
INSDC accession
* [Is_circular]: Flag to indicate circular regions
* gene types:
* ID: Unique identifier, format "gene:<gene_stable_id>"
* biotype: Ensembl biotype, e.g. "protein_coding", "pseudogene"
* gene_id: Ensembl gene stable ID
* version: Ensembl gene version
* [Name]: Gene name
* [description]: Gene description
* transcript types:
* ID: Unique identifier, format "transcript:<transcript_stable_id>"
* Parent: Gene identifier, format "gene:<gene_stable_id>"
* biotype: Ensembl biotype, e.g. "protein_coding", "pseudogene"
* transcript_id: Ensembl transcript stable ID
* version: Ensembl transcript version
* [Note]: If the transcript sequence has been edited (i.e. differs
from the genomic sequence), the edits are described in a note.
* exon
* Parent: Transcript identifier, format "transcript:<transcript_stable_id>"
* exon_id: Ensembl exon stable ID
* version: Ensembl exon version
* constitutive: Flag to indicate if exon is present in all
transcripts
* rank: Integer that show the 5'->3' ordering of exons
* CDS
* ID: Unique identifier, format "CDS:<protein_stable_id>"
* Parent: Transcript identifier, format "transcript:<transcript_stable_id>"
* protein_id: Ensembl protein stable ID
* version: Ensembl protein version
Metadata:
* 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 the release of this assembly e.g. 2009-02
* genome-build-accession - Genome accession e.g. GCA_000001405.14
* genebuild-last-updated - Date of the last genebuild update e.g. 2013-09
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FILE NAMES
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The files are consistently named following this pattern:
<species>.<assembly>.<_version>.gff3.gz
<species>: The systematic name of the species.
<assembly>: The assembly build name.
<version>: The version of Ensembl from which the data was exported.
gff3 : All files in these directories are in GFF3 format
gz : All files are compacted with GNU Zip for storage efficiency.
e.g.
Homo_sapiens.GRCh38.81.gff3.gz
For the predicted gene set, an additional abinitio flag is added to the name file.
<species>.<assembly>.<version>.abinitio.gff3.gz
e.g.
Homo_sapiens.GRCh38.81.abinitio.gff3.gz
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Example GFF3 output
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##gff-version 3
#!genome-build Pmarinus_7.0
#!genome-version Pmarinus_7.0
#!genome-date 2011-01
#!genebuild-last-updated 2013-04
GL476399 Pmarinus_7.0 supercontig 1 4695893 . . . ID=supercontig:GL476399;Alias=scaffold_71
GL476399 ensembl gene 2596494 2601138 . + . ID=gene:ENSPMAG00000009070;Name=TRYPA3;biotype=protein_coding;description=Trypsinogen A1%3B Trypsinogen a3%3B Uncharacterized protein [Source:UniProtKB/TrEMBL%3BAcc:O42608];logic_name=ensembl;version=1
GL476399 ensembl transcript 2596494 2601138 . + . ID=transcript:ENSPMAT00000010026;Name=TRYPA3-201;Parent=gene:ENSPMAG00000009070;biotype=protein_coding;version=1
GL476399 ensembl exon 2596494 2596538 . + . Name=ENSPMAE00000087923;Parent=transcript:ENSPMAT00000010026;constitutive=1;ensembl_end_phase=1;ensembl_phase=-1;rank=1;version=1
GL476399 ensembl exon 2598202 2598361 . + . Name=ENSPMAE00000087929;Parent=transcript:ENSPMAT00000010026;constitutive=1;ensembl_end_phase=2;ensembl_phase=1;rank=2;version=1
GL476399 ensembl exon 2599023 2599282 . + . Name=ENSPMAE00000087937;Parent=transcript:ENSPMAT00000010026;constitutive=1;ensembl_end_phase=1;ensembl_phase=2;rank=3;version=1
GL476399 ensembl exon 2599814 2599947 . + . Name=ENSPMAE00000087952;Parent=transcript:ENSPMAT00000010026;constitutive=1;ensembl_end_phase=0;ensembl_phase=1;rank=4;version=1
GL476399 ensembl exon 2600895 2601138 . + . Name=ENSPMAE00000087966;Parent=transcript:ENSPMAT00000010026;constitutive=1;ensembl_end_phase=-1;ensembl_phase=0;rank=5;version=1
GL476399 ensembl CDS 2596499 2596538 . + 0 ID=CDS:ENSPMAP00000009982;Parent=transcript:ENSPMAT00000010026
GL476399 ensembl CDS 2598202 2598361 . + 2 ID=CDS:ENSPMAP00000009982;Parent=transcript:ENSPMAT00000010026
GL476399 ensembl CDS 2599023 2599282 . + 1 ID=CDS:ENSPMAP00000009982;Parent=transcript:ENSPMAT00000010026
GL476399 ensembl CDS 2599814 2599947 . + 2 ID=CDS:ENSPMAP00000009982;Parent=transcript:ENSPMAT00000010026
GL476399 ensembl CDS 2600895 2601044 . + 0 ID=CDS:ENSPMAP00000009982;Parent=transcript:ENSPMAT00000010026
GL476399 ensembl five_prime_UTR 2596494 2596498 . + . Parent=transcript:ENSPMAT00000010026
GL476399 ensembl three_prime_UTR 2601045 2601138 . + . Parent=transcript:ENSPMAT00000010026