diff --git a/etc/feature_keys_gff b/etc/feature_keys_gff index 8a4876bec3bdc817fce76f2d883ad94fed2eea52..be96c49d82497c555e315f6e53f5686bee61f2be 100644 --- a/etc/feature_keys_gff +++ b/etc/feature_keys_gff @@ -5,37 +5,37 @@ # # key Qualifiers (@=mandatory) # ======= ======================== -region ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -contig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -supercontig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -chromosome ID Name Alias Parent Note note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -gene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -CDS ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -polypeptide ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -pseudogene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -intron ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -exon ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score -three_prime_UTR ID Alias Parent Note systematic_id db_xref note -five_prime_UTR ID Alias Parent Note systematic_id db_xref note +region ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +contig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +supercontig ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +chromosome ID Name Alias Parent Note note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +gene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +CDS ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +polypeptide ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref Product molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color mass isoelectric charge +pseudogene ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +intron ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +exon ID Name Alias Parent Note description locus stable_id ec_number gene_symbol Ontology_term Dbxref molecule_type size organism_name strain translation_table topology localization gff_source gff_seqname score colour color +three_prime_UTR ID Alias Parent Note systematic_id db_xref note colour color +five_prime_UTR ID Alias Parent Note systematic_id db_xref note colour color transcript -primary_transcript ID Name Alias Parent Note db_xref product note controlled_curation -tRNA ID Name Alias Parent Note db_xref product note controlled_curation -rRNA ID Name Alias Parent Note db_xref product note controlled_curation -mRNA ID Name Alias Parent Note db_xref product note controlled_curation -snRNA ID Name Alias Parent Note db_xref product note controlled_curation -scRNA ID Name Alias Parent Note db_xref product note controlled_curation -snoRNA ID Name Alias Parent Note db_xref product note controlled_curation -polypeptide_domain ID Name Alias Parent Note -signal_peptide ID Name Alias Parent Note -matches ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score -translated_nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -protein_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -sequence_difference ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -repeat_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -direct_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -inverted_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -dispersed_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term -repeat_family ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score -transposable_element ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term -binding_site ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term +primary_transcript ID Name Alias Parent Note db_xref product note controlled_curation colour color +tRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +rRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +mRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +snRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +scRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +snoRNA ID Name Alias Parent Note db_xref product note controlled_curation colour color +polypeptide_domain ID Name Alias Parent Note colour color +signal_peptide ID Name Alias Parent Note colour color +matches ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score colour color +translated_nucleotide_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +protein_match ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +sequence_difference ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +repeat_region ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +direct_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +inverted_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +dispersed_repeat ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term colour color +repeat_family ID Name Alias Parent Note Target Gap Derives_from Dbxref Ontology_term gff_source gff_seqname score colour color +transposable_element ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term colour color +binding_site ID Name Alias Parent Target Gap Derives_from Note Dbxref Ontology_term colour color diff --git a/etc/qualifier_types_gff b/etc/qualifier_types_gff index 75abc93638f769a3b9968805b87f216154b63a51..3e7bdd5b427dd108a1298e2ad6ecddd71b164d89 100644 --- a/etc/qualifier_types_gff +++ b/etc/qualifier_types_gff @@ -28,6 +28,7 @@ Name no text Alias no text Parent no text Note no "text" +Product no "text" description no text Ontology_term no text gff_source no text @@ -37,89 +38,10 @@ Target no text Gap no text Derives_from no text Dbxref no "text" -# -allele no "text" -anticodon yes (::) pos aa -bound_moiety no "text" -cell_line no "text" -cell_type no "text" -chromosome no "opt" -citation no ref -clone no "text" -clone_lib no "text" -codon no (::) seq aa -codon_start yes number 1 3 -cons_splice yes (::) 5'site 3'site -country no "text" -cultivar no "text" -db_xref no "text" -dev_stage no "text" -direction yes list LEFT RIGHT BOTH -ecotype no "text" -EC_number no "text" -environmental_sample no none -estimated_length no "text" -evidence yes list EXPERIMENTAL NOT_EXPERIMENTAL -exception no "text" -focus no none -frequency yes real 0.0 1.0 -function yes "text" -gene no "text" -germline yes none -haplotype no "text" -insertion_seq no "text" -isolation_source no "text" -isolate no "text" -kinetoplast no "opt" -label yes item -lab_host no "text" -locus_tag no "text" -macronuclear no none -map no "text" -mod_base no modbase -mol_type no "text" -note no "text" -number yes number 1 99999999 -operon no "text" -organell no "text" -organism yes "text" -partial yes none -PCR_conditions no "text" -phenotype no "text" -plasmid no "text" -pop_variant no "text" -product no "text" -protein_id no "text" -proviral yes none -pseudo yes none -rearranged yes none -replace no "text" -rpt_family no "text" -rpt_type no list TANDEM INVERTED FLANKING TERMINAL DIRECT \ - DISPERSED OTHER -rpt_unit no location -segment no "text" -sequenced_mol no "list" "cDNA" "cDNA to genomic RNA" \ - "cDNA to mRNA" "cDNA to other RNA" \ - "cDNA to rRNA" "DNA" "mRNA" \ - "RNA" "rRNA" "scRNA" "snRNA" "tRNA" -serotype no "text" -serovar no "text" -sex no "text" -specific_host no "text" -specimen_voucher no "text" -standard_name no "text" -strain no "text" -sub_clone no "text" -sub_species no "text" -sub_strain no "text" -tissue_lib no "text" -tissue_type no "text" -transgenic no "text" -translation no "text" -transl_except no (::) pos aa -transl_table no number 1 11 -transposon no "text" -usedin no feature -variety no "text" -virion no none +polypeptide no text +polypeptide_domain no text +colour no text +color no text +mass no text +isoelectric no text +charge no text