GFF2 features

From WormBaseWiki
Jump to: navigation, search

This 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