GFF2 features
From WormBaseWiki
Jump to navigationJump to searchThis page describes genomic annotations found in WormBase's GFF2 genome feature tables.
| ALLELE:. | 14814 |
| cDNA_match:BLAT_mRNA_BEST | 24512 |
| cDNA_match:BLAT_mRNA_OTHER | 8559 |
| CDS:curated | 23273 |
| CDS:Genefinder | 21182 |
| CDS:GeneMarkHMM | 24016 |
| CDS:history | 8893 |
| CDS:mSplicer_orf | 26582 |
| CDS:mSplicer_transcript | 26582 |
| CDS:twinscan | 21681 |
| Clone_left_end:. | 2795 |
| Clone_right_end:. | 2708 |
| coding_exon:Coding_transcript | 169128 |
| coding_exon:curated | 148639 |
| coding_exon:Genefinder | 133896 |
| coding_exon:GeneMarkHMM | 132967 |
| coding_exon:history | 64715 |
| coding_exon:mSplicer_orf | 168585 |
| coding_exon:mSplicer_transcript | 171688 |
| coding_exon:Transposon_CDS | 532 |
| coding_exon:twinscan | 124073 |
| complex_change_in_nucleotide_sequence:Allele | 1181 |
| deletion:Allele | 3215 |
| EST_match:BLAT_EST_BEST | 936193 |
| EST_match:BLAT_EST_OTHER | 459402 |
| exon:Coding_transcript | 173812 |
| exon:curated | 148639 |
| exon:Genefinder | 133896 |
| exon:GeneMarkHMM | 132967 |
| exon:history | 65140 |
| exon:miRNA | 140 |
| exon:mSplicer_orf | 168585 |
| exon:mSplicer_transcript | 171688 |
| exon:ncRNA | 39 |
| exon:Non_coding_transcript | 539 |
| exon:Pseudogene | 3438 |
| exon:rRNA | 8 |
| exon:scRNA | 1 |
| exon:snlRNA | 4 |
| exon:snoRNA | 128 |
| exon:snRNA | 82 |
| exon:Transposon | 2 |
| exon:Transposon_CDS | 532 |
| exon:tRNA | 22 |
| exon:tRNAscan-SE-1.23 | 637 |
| exon:twinscan | 124073 |
| experimental_result_region:cDNA_for_RNAi | 2828 |
| experimental_result_region:Expr_profile | 17360 |
| expressed_sequence_match:BLAT_OST_BEST | 106072 |
| expressed_sequence_match:BLAT_OST_OTHER | 106158 |
| five_prime_UTR:Coding_transcript | 16816 |
| gene:curated | 19754 |
| gene:gene | 22364 |
| gene:landmark | 113 |
| gmap_span:absolute_pmap_position | The absolute coordinates of genetic map features that have been placed onto the physical map (ie cloned loci) |
| gmap_span:interpolated_pmap_position | The estimated maximal extents for genetic loci interpolated into phsyical map coordinates. Coordinates are established based on two- and three-factor mapping data. |
| insertion:Allele | 21 |
| intron:. | 1016 |
| intron:Coding_transcript | 147048 |
| intron:curated | 125366 |
| intron:Genefinder | 112714 |
| intron:history | 56150 |
| intron:ncRNA | 2 |
| intron:Non_coding_transcript | 433 |
| intron:Pseudogene | 2227 |
| intron:Transposon | 1 |
| intron:Transposon_CDS | 292 |
| intron:twinscan | 102393 |
| inverted_repeat:inverted | 99252 |
| miRanda:binding_site | 61431 |
| miRNA_primary_transcript:miRNA | 140 |
| misc_feature:binding_site | 154 |
| Motif:translated_feature | 138683 |
| motif_segment:translated_feature | 293694 |
| nc_primary_transcript:Non_coding_transcript | 106 |
| ncRNA_primary_transcript:ncRNA | 37 |
| nucleotide_match:BLAT_ncRNA_BEST | 51 |
| nucleotide_match:BLAT_ncRNA_OTHER | 5 |
| nucleotide_match:BLAT_TC1_BEST | 1076 |
| nucleotide_match:BLAT_TC1_OTHER | 4247 |
| nucleotide_match:TEC_RED | 8793 |
| nucleotide_match:waba_coding | 289860 |
| nucleotide_match:waba_strong | 378414 |
| nucleotide_match:waba_weak | 938690 |
| oligo:. | 45160 |
| operon:operon | 1123 |
| PCR_product:GenePair_STS | 46249 |
| PCR_product:Orfeome | 19389 |
| PCR_product:Promoterome | 6598 |
| PicTar:binding_site | 5917 |
| polyA_signal_sequence:polyA_signal_sequence | 2454 |
| polyA_site:polyA_site | 3028 |
| processed_transcript:gene | 20573 |
| protein_coding_primary_transcript:Coding_transcript | 7 |
| protein_match:wublastx | 1247517 |
| Pseudogene:history | 66 |
| Pseudogene:Pseudogene | 1210 |
| reagent:Expr_pattern | 2230 |
| reagent:Oligo_set | 83900 |
| region:Genbank | 3267 |
| region:Genomic_canonical | 3267 |
| region:Link | 25 |
| region:Vancouver_fosmid | 12869 |
| repeat_region:RepeatMasker | 77966 |
| RNAi_reagent:RNAi_primary | 139291 |
| RNAi_reagent:RNAi_secondary | 14131 |
| RNAz:ncRNA | 3672 |
| rRNA_primary_transcript:rRNA | 8 |
| SAGE_tag:SAGE_tag | 85639 |
| SAGE_tag:SAGE_tag_genomic_unique | 70768 |
| SAGE_tag:SAGE_tag_most_three_prime | 8455 |
| SAGE_tag:SAGE_tag_unambiguously_mapped | 72695 |
| scRNA_primary_transcript:scRNA | 1 |
| Sequence:. | 3 |
| sequence_variant:Allele | 1 |
| SL1_acceptor_site:SL1 | 7664 |
| SL2_acceptor_site:SL2 | 2053 |
| snoRNA_primary_transcript:snoRNA | 128 |
| SNP:Allele | 15058 |
| snRNA_primary_transcript:snRNA | 82 |
| substitution:Allele | 1940 |
| tandem_repeat:tandem | 38996 |
| three_prime_UTR:Coding_transcript | 14305 |
| Transcript:Coding_transcript | 26757 |
| Transcript:history | 32 |
| Transcript:snlRNA | 4 |
| translated_nucleotide_match:BLAT_NEMATODE | 917760 |
| translated_nucleotide_match:BLAT_NEMBASE | 447492 |
| translated_nucleotide_match:BLAT_WASHU | 845075 |
| translated_nucleotide_match:mass_spec_genome | 55225 |
| transposable_element:Transposon | 99 |
| transposable_element:Transposon_CDS | 240 |
| transposable_element_insertion_site:Allele | 1503 |
| transposable_element_insertion_site:Mos_insertion_allele | 5099 |
| tRNA_primary_transcript:tRNA | 22 |
| tRNA_primary_transcript:tRNAscan-SE-1.23 | 608 |
