Schema for WormBase RNAs - WormBase RNA Annotations
  Database: ce6    Primary Table: sangerRnaGene    Row Count: 6,440   Data last updated: 2008-06-03
Format description: A gene prediction.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name Y74C9A.6varchar(255) values Name of gene
chrom chrIvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3746int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3909int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3909int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3909int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 3746,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3909,longblob   Exon end positions (or start positions for minus strand item)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
585Y74C9A.6chrI-374639093909390913746,3909,
585F53G12.12chrI+1112911114251114251114251111291,111425,
590Y18H1A.t1chrI+7546817547657547657547651754681,754765,
592Y95B8A.t1chrI-9460459461179461179461171946045,946117,
596F47G6.t1chrI+144713814472111447211144721111447138,1447211,
597Y92H12A.t1chrI+157572015757931575793157579311575720,1575793,
598Y71G12B.29chrI+173865017386741738674173867411738650,1738674,
600Y37E3.22chrI-206988520700252070025207002512069885,2070025,
600Y37E3.21chrI-207025720703962070396207039612070257,2070396,
600Y37E3.20chrI+208503820851572085157208515712085038,2085157,

Note: all start coordinates in our database are 0-based, not 1-based. See explanation here.

WormBase RNAs (sangerRnaGene) Track Description
 

Description

The WormBase Genes track shows RNA predictions from the Wormbase v. WS190 files downloaded from the Sanger Institute FTP site. This track shows the subset of data annotated as "miRNA", "ncRNA", "rRNA", "scRNA", "snRNA" ,"snlRNA" ,"snoRNA" ,"tRNA", or "tRNAscan-SE-1.23" in the gff files.

Credits

The Sanger gene predictions are produced by WormBase. Thanks to the WormBase Consortium for providing these data.