Index of /download/gff

Icon  Name                       Last modified      Size  Description
[DIR] Parent Directory - [DIR] A_acidus_CBS_106_47/ 16-Dec-2013 10:46 - [DIR] A_aculeatus_ATCC16872/ 16-Dec-2013 10:52 - [DIR] A_brasiliensis_CBS_101740/ 16-Dec-2013 10:57 - [DIR] A_carbonarius_ITEM_5010/ 16-Dec-2013 11:04 - [DIR] A_clavatus_NRRL_1/ 16-Dec-2013 12:01 - [DIR] A_flavus_NRRL_3357/ 16-Dec-2013 12:05 - [DIR] A_fumigatus_A1163/ 16-Dec-2013 11:09 - [DIR] A_fumigatus_Af293/ 26-Oct-2014 07:06 - [DIR] A_glaucus_CBS_516_65/ 16-Dec-2013 11:17 - [DIR] A_kawachii/ 16-Dec-2013 11:20 - [DIR] A_nidulans_FGSC_A4/ 12-Oct-2014 07:05 - [DIR] A_niger_ATCC_1015/ 25-Nov-2013 14:12 - [DIR] A_niger_CBS_513_88/ 31-Aug-2014 07:06 - [DIR] A_oryzae_RIB40/ 02-Mar-2014 07:25 - [DIR] A_sydowii/ 16-Dec-2013 11:23 - [DIR] A_terreus_NIH2624/ 16-Dec-2013 12:13 - [DIR] A_tubingensis_CBS_134_48/ 16-Dec-2013 11:31 - [DIR] A_versicolor/ 16-Dec-2013 11:39 - [DIR] A_wentii_DTO_134E9/ 16-Dec-2013 11:47 - [DIR] A_zonatus/ 16-Dec-2013 11:56 - [DIR] N_fischeri_NRRL_181/ 16-Dec-2013 12:17 -
Sub-directories within this directory contain data for various Aspergillus 
species in the Generic Feature Format (GFF). These files describe features, 
including chromosomes, ORFs, CDSs, introns, sequence gaps, intergenic regions, etc.

Please see http://www.sequenceontology.org/gff3.shtml for a detailed description 
of the Generic Feature Format (GFF).


A_nidulans_FGSC_A4/ contains the data for the current AspGD annotation of the 
A. nidulans genome sequence.  These files are updated weekly.  This directory 
also contains historic annotation from previous assemblies.

A_fumigatus_Af293/ contains the data for the current AspGD annotation of the 
A. fumigatus genome sequence.  These files are updated weekly.  

A_niger_CBS_513_88/ contains the data for the current AspGD annotation of the 
A. niger genome sequence.  These files are updated weekly.

A_oryzae_RIB40/ contains the data for the current AspGD annotation of the
A. oryzae genome sequence.  These files are updated weekly.

The remaining directories contain annotation information for
Aspergillus-related species and strains which are not actively 
curated by AspGD at this time.  These files are updated sporadically,
as new gene models become available.


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GFF files are in the canonical GFF3 format specifications as of October 2012.

Introns are no longer listed, but can be inferred by comparing exons to
transcripts.

5' and 3' untranslated regions (UTRs) are no longer listed, but can be
inferred by comparing CDS to exons.

Below are listed the relationship heirarchies for various feature types.
The type of a given feature is given in column 3, and its parent feature is
given in column 9.

Protein-coding genes:
Type = 'gene', parent of 'mRNA'
Type = 'mRNA', parent of 'exon'
Type = 'exon', parent of 'CDS'
Type = 'CDS', no children

Upstream open reading frame (uORF):
Listed as CDS of parent gene, with column 9 attribute "parent_feature_type=uORF"

Non-coding RNAs (tRNA, rRNA, snRNA, etc.):
Type = 'gene', parent of 'tRNA' (or rRNA, snRNA, etc.)
Type = 'tRNA' (or rRNA, snRNA, etc.), parent of 'exon'
Type = 'exon', no children

Non-transcribed feature (repeat_region, centromere, etc):
Type = repeat_region (or centromere, etc.), no children

Pseudogene of protein-coding genes:
Type = 'pseudogene', parent of 'mRNA'
Type = 'mRNA', parent of 'exon'
Type = 'exon', parent of 'CDS'
Type = 'CDS', no children

Pseudogene of non-coding RNAs (tRNA, rRNA, snRNA, etc.):
Type = 'pseudogene', parent of 'tRNA' (or rRNA, snRNA, etc.)
Type = 'tRNA' (or rRNA, snRNA, etc.), parent of 'exon'
Type = 'exon', no children