GFF3 features (C. briggsae)

From WormBaseWiki
Jump to: navigation, search

This article describes features included in the C. briggsae GFF3 files. For introduction information on the GFF3 files, please see [[GFF3_features GFF3 features] article.

The WormBase C. briggsae GFF3 files can be downloaded from:

ftp://ftp.wormbase.org/pub/wormbase/genomes/briggsae/genome_feature_tables/GFF3

The attribute tags (column 9) for each feature group are listed in parenthesis. Some attributes listed for a feature group may not be available for each feature within the group.

FEATURES

  • The source field for coding gene features is "Coding_transcript". CDS, mRNA, exon and introns are available.
CDS:Coding_transcript                              (ID,Note,brigpep,ortholog,predicted_once,supported_by_multiple_predictions,
                                                    supported_by_ortholog,supported_by_paralogs)
mRNA:Coding_transcript                             (ID)
exon:Coding_transcript                             (Parent)
intron:Coding_transcript                           (Parent,cds)
  • Retired genes: a CDS feature is included. The CDS features consist of multiple parts and are unified by a common ID atribute.
CDS:history                                        (ID)
  • Non-coding genes: ncRNA and exons are available.
ncRNA:ncRNA                                        (ID)
exon:ncRNA                                         (Parent)
  • Alignment features: These features consist of multiple parts unified by a common ID attribute.
nucleotide_match:BLAT_BAC_END                      (ID,Target)
nucleotide_match:BLAT_EST_BEST                     (ID,Target)
nucleotide_match:BLAT_EST_OTHER                    (ID,Target)
nucleotide_match:BLAT_NEMATODE                     (ID,Target)
nucleotide_match:BLAT_OST_BEST                     (ID,Target)
nucleotide_match:BLAT_OST_OTHER                    (ID,Target)
nucleotide_match:BLAT_WASHU                        (ID,Target)
nucleotide_match:BLAT_briggsae_est                 (ID,Target)
nucleotide_match:BLAT_elegans_est                  (ID,Target)
nucleotide_match:BLAT_elegans_mrna                 (ID,Target)
nucleotide_match:BLAT_elegans_ost                  (ID,Target)
nucleotide_match:BLAT_mRNA_BEST                    (ID,Target)
nucleotide_match:BLAT_mRNA_OTHER                   (ID,Target)
nucleotide_match:waba_coding                       (ID,Target)
nucleotide_match:waba_strong                       (ID,Target)
nucleotide_match:waba_weak                         (ID,Target)
nucleotide_match:wublastx                          (ID,Target)
  • Other: The remaining features are listed below.

RFLP_fragment:predicted (methods,num_reads,polymorphism) SNP:Allele (variation) chromosome:Reference (ID,Name) region:Genomic_canonical (Name,sequence) region:contig (Name,sequence)

CHANGES

WS176 - initial GFF3 and start documentation