Schema for WS245 Genes - Gene predictions from WormBase WS245 release
  Database: ce11    Primary Table: ws245Genes    Row Count: 57,827   Data last updated: 2016-02-25
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name Y74C9A.6varchar(255) values Name of gene (usually transcript_id from GTF)
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)
score 0int(11) range score
name2 WBGene00023193varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat noneenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        ce11.ws245GenesPeptide.name (via ws245Genes.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585Y74C9A.6chrI-374639093909390913746,3909,0WBGene00023193nonenone-1,
585Y74C9A.3chrI-41181023042201014854118,5194,6036,9726,10094,4358,5296,6327,9846,10230,0WBGene00022277cmplcmpl0,0,0,0,0,
585Y74C9A.2a.2chrI+10412168421164016585410412,11617,14950,16472,10585,11689,15160,16842,0WBGene00022276cmplcmpl-1,0,1,1,
585Y74C9A.2b.2chrI+11494167931510216585511494,11617,14950,16472,16701,11561,11689,15160,16585,16793,0WBGene00022276cmplcmpl-1,-1,0,1,-1,
585Y74C9A.2b.4chrI+11498168421510216585411498,11617,14950,16472,11557,11689,15160,16842,0WBGene00022276cmplcmpl-1,-1,0,1,
585Y74C9A.2b.1chrI+11498168421510216585411498,11617,14950,16472,11561,11689,15160,16842,0WBGene00022276cmplcmpl-1,-1,0,1,
585Y74C9A.2a.3chrI+11504168421164016585411504,11622,14950,16472,11561,11689,15160,16842,0WBGene00022276cmplcmpl-1,0,1,1,
585Y74C9A.2a.1chrI+11617168421164016585311617,14950,16472,11689,15160,16842,0WBGene00022276cmplcmpl0,1,1,
585Y74C9A.2b.3chrI+11622168421510216585311622,14949,16472,11686,15160,16842,0WBGene00022276cmplcmpl-1,0,1,
585Y74C9A.4bchrI-174822677817910267781217482,18005,19014,20270,20847,21012,24650,24928,25272,26370,26589,26732,17958,18115,19241,20478,20964,21139,24845,25090,25472,26524,26690,26778,0WBGene00022278cmplcmpl0,1,2,1,1,0,0,0,1,0,1,0,

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

WS245 Genes (ws245Genes) Track Description
 

Description

These gene predictions were generated by WormBase.

Methods

These gene predictions were produced and hand-curated by WormBase. For a detailed description of the methods, refer to Howe et al. (2016) in the References section below.

Credits

Thanks to WormBase for providing this annotation.

References

Howe KL, Bolt BJ, Cain S, Chan J, Chen WJ, Davis P, Done J, Down T, Gao S, Grove C et al. WormBase 2016: expanding to enable helminth genomic research. Nucleic Acids Res. 2016 Jan 4;44(D1):D774-80. PMID: 26578572; PMC: PMC4702863