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[Gusdev-gusdev] RE: GUS features
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From: Matthew B. <mb...@sa...> - 2002-12-03 19:21:16
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Chris=20 Here is my attempt to map GUS to SO (I've also attached it as because I'm not sure how well my browser preserves the tabs) There are some big gaps, such as "source", protein features and miscellaneous features. Cheers Matt ... SUBCLASS_VIEW =09 <BindingSiteFeature: names of binding sites> =09 CentromereFeature: =09 predicted centromere ???? SO:0000577 centromere DNARegulatory: =09 -10_signal SO:0000175 -10 signal -35_signal SO:0000176 -35 signal CAAT_signal SO:0000172 CAAT signal GC_signal SO:0000173 GC-rich region TATA_signal SO:0000174 TATA box attenuator SO:0000140 attenuator enhancer SO:0000165 enhancer * promoter SO:0000167 promoter * terminator SO:0000141 terminator * DNAStructure: =09 D-loop SO:0000297 D-loop primer_bind ???? SO:0005850 primer binding site (sub-class of LTR-retrotransposon) rep_origin SO:0000296 origin of replication ExonFeature =09 ExonFeature SO:0000147 exon * GeneFeature =09 CDS ???? SO:0001254 coding sequence predicted GeneFeature SO:0000704 gene element gene SO:0000008 gene (sensu yourfavoriteorganism) snRNA SO:0000274 small nuclear RNA tRNA SO:0000253 transfer RNA HexamerFeature =09 hexamer ???? =09 Immunoglobulin SO:0000460 vertebrate immunoglobulin/T-cell receptor gene C-region ???? SO:0000478 C-gene D_segment ???? SO:0000458 D-gene J_segment ???? SO:0000470 J-gene N_region ???? =09 S_region ???? =09 V_region ???? SO:0000466 V-gene V_segment ???? =09 iDNA ???? =09 LowComplexityNAFeature =09 low complexity sequence ???? =09 Miscellaneous =09 misc_binding ???? =09 misc_feature ???? =09 misc_signal ???? =09 protein_bind ???? =09 stem_loop SO:0000313 stem loop unsure ???? =09 PolyAFeature =09 PolyAFeature ???? SO:0000610 polyA sequence ???? SO:0000553 polyA site PromoterFeature =09 PromoterFeature ???? How does this differ from DNARegulatory>Promoter ? differ from DNARegulatory>Promoter ? various promoter sets ???? =09 ProteinFeature =09 mat_peptide ???? N/A =09 sig_peptide ???? N/A =09 transit_peptide ???? N/A =09 RNAFeature =09 PREDICTED REFSEQ ???? =09 PROVISIONAL REFSEQ ???? =09 REFSEQ ???? =09 REVIEWED REFSEQ ???? =09 RNAFeature ???? SO:0000184 transcript region assembly ???? =09 mRNA SO:0000234 messenger RNA RNAStructure =09 RBS SO:0000552 5'-ribosome binding site misc_RNA ???? =09 RNAType =09 rRNA ???? is this different to the GeneFeature>rRNA? =09 scRNA ???? =09 snRNA ???? is this different to the GeneFeature>rRNA? =09 tRNA ???? is this different to the GeneFeature>rRNA? =09 <Repeats: names of repeats> =09 RestrictionFragmentFeature =09 RestrictionFragmentFeature ???? Is this to describe the DNA source? =09 <SAGETagFeature: locations on chromosomes> =09 STS =09 STS ???? =09 ScaffoldGapFeature =09 assembly gap ???? =09 SeqVariation =09 SNP SO:0000694 single nucleotide polymorphism allele ???? =09 conflict ???? =09 misc_difference ???? =09 misc_recomb ???? =09 modified_base SO:0000199 modified DNA base feature mutation ???? SO:1000170 uncharacterised chromosomal mutation old_sequence ???? =09 variation SO:1000128 sequence variation feature Source =09 source ???? =09 TandemRepeatFeature =09 tandem repeat SO:0000705 tandem repeat TelomereFeature =09 predicted telomere ???? SO:0000624 telomere Transcript SO:0000673 transcript 3'UTR SO:0000205 3'-untranslated region 3'clip SO:0000557 3'-clip 5'UTR SO:0000204 5'-untranslated region 5'clip SO:0000555 5'-clip CDS ???? SO:0001254 coding sequence predicted exon SO:0000147 exon intron SO:0000188 intron mRNA SO:0000234 messenger RNA polyA_signal SO:0000551 polyA signal sequence precursor_RNA ???? =09 prim_transcript SO:0000185 primary transcript > -----Original Message----- > From: Chris Stoeckert [mailto:sto...@pc...]=20 > Sent: 26 November 2002 19:37 > To: Matthew Berryman > Cc: gusdev-gusdev > Subject: Re: GUS features >=20 >=20 > Hi Matt, > I've generated a list of the 26 subclass views of NAFeatureImp and=20 > looked at the distinct names associated with. These are given below.=20 > Will now start looking at the SO and SO lite for these. > Chris >=20 > On Friday, November 22, 2002, at 12:59 PM, Matt Berriman wrote: >=20 > > Hi Chris > > Do you have a list of GUS sequence features? The SO group are > > preparing a "SO Lite" -- it would be good to check that=20 > everything is=20 > > represented. > > > > cheers > > Matt >=20 > SUBCLASS_VIEW > <BindingSiteFeature: names of binding sites> > CentromereFeature: > predicted centromere > DNARegulatory: > -10_signal > -35_signal > CAAT_signal > GC_signal > TATA_signal > attenuator > enhancer > promoter > terminator > DNAStructure: > D-loop > primer_bind > rep_origin > ExonFeature > ExonFeature > GeneFeature > CDS > GeneFeature > gene > snRNA > tRNA > HexamerFeature > hexamer > Immunoglobulin > C-region > D_segment > J_segment > N_region > S_region > V_region > V_segment > iDNA > LowComplexityNAFeature > low complexity sequence > Miscellaneous > misc_binding > misc_feature > misc_signal > protein_bind > stem_loop > unsure > PolyAFeature > PolyAFeature > PromoterFeature > PromoterFeature > various promoter sets > ProteinFeature=09 > mat_peptide > sig_peptide > transit_peptide > RNAFeature > PREDICTED REFSEQ > PROVISIONAL REFSEQ > REFSEQ > REVIEWED REFSEQ > RNAFeature > assembly > mRNA > RNAStructure > RBS > misc_RNA > RNAType > rRNA > scRNA > snRNA > tRNA > <Repeats: names of repeats> > RestrictionFragmentFeature > RestrictionFragmentFeature > <SAGETagFeature: locations on chromosomes> > STS > STS > ScaffoldGapFeature > assembly gap > SeqVariation > SNP > allele > conflict > misc_difference > misc_recomb > modified_base > mutation > old_sequence > variation > Source > source > TandemRepeatFeature > tandem repeat > TelomereFeature > predicted telomere > Transcript > 3'UTR > 3'clip > 5'UTR > 5'clip > CDS > exon > intron > mRNA > polyA_signal > precursor_RNA > prim_transcript >=20 >=20 |
