diff --git a/etc/feature_keys_gff b/etc/feature_keys_gff index 639ec7d7d86b48078a479ae8893f1050e057cf05..85e208ed5b78c1133cfb44c169da762a1a90b435 100644 --- a/etc/feature_keys_gff +++ b/etc/feature_keys_gff @@ -8,25 +8,25 @@ region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score contig ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score supercontig ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score -chromosome ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score +chromosome ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified note comment description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score gene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score -CDS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified codon_start description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score results note job +CDS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified codon_start description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score results note comment job polypeptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref product molecule_type size organism_name strain topology localization gff_source gff_seqname score mass isoelectric charge source pseudogene ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score pseudogenic_exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score pseudogenic_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score intron ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score exon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified codon_start description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain topology localization gff_source gff_seqname score -three_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified systematic_id db_xref note -five_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified systematic_id db_xref note +three_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified systematic_id db_xref note comment +five_prime_UTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified systematic_id db_xref note comment transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified -primary_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -tRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -rRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -mRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -snRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -scRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation -snoRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note controlled_curation +primary_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +tRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +rRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +mRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +snRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +scRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation +snoRNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified db_xref product note comment controlled_curation polypeptide_domain ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified signal_peptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @@ -41,37 +41,37 @@ repeat_family ID Name Alias Parent Note Target Gap Derives_from Dbxref Ont transposable_element ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term feature_id timelastmodified binding_site ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term feature_id timelastmodified -minus_10_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial standard_name -minus_35_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial standard_name -three_prime_clip ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note partial standard_name -five_prime_clip ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note partial standard_name -CAAT_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial -D_loop ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial -GC_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial -three_prime_LTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note partial standard_name -five_prime_LTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note partial standard_name -N_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation codon codon_start db_xref evidence gene label locus_tag map note partial product pseudo standard_name -STS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial standard_name -TATA_box ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial -attenuator ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note operon partial phenotype -enhancer ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial standard_name +minus_10_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial standard_name +minus_35_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial standard_name +three_prime_clip ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment partial standard_name +five_prime_clip ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment partial standard_name +CAAT_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial +D_loop ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial +GC_signal ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial +three_prime_LTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment partial standard_name +five_prime_LTR ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment partial standard_name +N_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation codon codon_start db_xref evidence gene label locus_tag map note comment partial product pseudo standard_name +STS ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial standard_name +TATA_box ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial +attenuator ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment operon partial phenotype +enhancer ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial standard_name gap ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @estimated_length -iDNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note number partial standard_name -mature_peptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified EC_number allele citation codon codon_start db_xref evidence function gene label locus_tag map note partial product pseudo standard_name -modified_base_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @mod_base allele citation db_xref evidence frequency gene label locus_tag map note -operon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @operon allele citation db_xref evidence function label map note phenotype pseudo standard_name -polyA_signal_sequence ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial -polyA_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note -precursor_RNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial product standard_name -primary_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial standard_name -primer_binding_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified PCR_conditions allele citation db_xref evidence gene label locus_tag map note partial standard_name -promoter ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial phenotype pseudo standard_name -protein_binding_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @bound_moiety allele citation db_xref evidence function gene label locus_tag map note partial standard_name -origin_of_replication ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref direction evidence gene label locus_tag map note partial standard_name -repeat_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene insertion_seq label locus_tag map note partial rpt_family rpt_type rpt_unit standard_name DNA_transposon -repeat_unit ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note partial rpt_family rpt_type rpt_unit -satellite_DNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note partial rpt_family rpt_type rpt_unit standard_name -stem_loop ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note operon partial standard_name -terminator ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note operon partial standard_name -transit_peptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation codon codon_start db_xref evidence function gene label locus_tag map note partial product pseudo standard_name +iDNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment number partial standard_name +mature_peptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified EC_number allele citation codon codon_start db_xref evidence function gene label locus_tag map note comment partial product pseudo standard_name +modified_base_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @mod_base allele citation db_xref evidence frequency gene label locus_tag map note comment +operon ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @operon allele citation db_xref evidence function label map note comment phenotype pseudo standard_name +polyA_signal_sequence ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial +polyA_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment +precursor_RNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial product standard_name +primary_transcript ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial standard_name +primer_binding_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified PCR_conditions allele citation db_xref evidence gene label locus_tag map note comment partial standard_name +promoter ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial phenotype pseudo standard_name +protein_binding_site ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified @bound_moiety allele citation db_xref evidence function gene label locus_tag map note comment partial standard_name +origin_of_replication ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref direction evidence gene label locus_tag map note comment partial standard_name +repeat_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene insertion_seq label locus_tag map note comment partial rpt_family rpt_type rpt_unit standard_name DNA_transposon +repeat_unit ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment partial rpt_family rpt_type rpt_unit +satellite_DNA ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment partial rpt_family rpt_type rpt_unit standard_name +stem_loop ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence function gene label locus_tag map note comment operon partial standard_name +terminator ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation db_xref evidence gene label locus_tag map note comment operon partial standard_name +transit_peptide ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term feature_id timelastmodified allele citation codon codon_start db_xref evidence function gene label locus_tag map note comment partial product pseudo standard_name diff --git a/etc/qualifier_types_gff b/etc/qualifier_types_gff index 5ca84645b36ad1e007a208f76935e857c83c1536..bbbdf56baf2857555b55a9d9fe18b598a597b633 100644 --- a/etc/qualifier_types_gff +++ b/etc/qualifier_types_gff @@ -59,6 +59,7 @@ clone no "text" clone_lib no "text" codon no (::) seq aa codon_start yes number 1 3 +comment no "text" cons_splice yes (::) 5'site 3'site country no "text" cultivar no "text"