Schema for xenoRefGene
  Database: droAna1    Primary Table: xenoRefGene    Row Count: 284,592   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 588smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001080477varchar(255) values Name of gene (usually transcript_id from GTF)
chrom 2448870varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 413850int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 417203int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 413850int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 417203int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 413850,416792,416924,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 413994,416876,417203,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 TENM3varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        droAna1.all_mrna.qName (via xenoRefGene.name)
      droAna1.xenoMrna.qName (via xenoRefGene.name)
      droAna1.xenoRefFlat.name (via xenoRefGene.name)
      droAna1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
588NM_0010804772448870-4138504172034138504172033413850,416792,416924,413994,416876,417203,0TENM3incmplincmpl0,0,0,
602NM_0012758682448894+234711323492712347116234897552347113,2347661,2348432,2348921,2349232,2347146,2348370,2348614,2348979,2349271,0AnxB9cmplcmpl0,0,1,0,-1,
601NM_0276692448902+216956321705802169563217017342169563,2169752,2170086,2170508,2169641,2169905,2170173,2170580,0Septin12incmplincmpl0,0,0,-1,
604NM_0010218642448840+255247225529702552472255297032552472,2552670,2552895,2552490,2552802,2552970,0ned8cmplincmpl0,0,0,
9NM_0013005262448902+312023033234183198456332341863120230,3120349,3121622,3198456,3323334,3323385,3120257,3120353,3121637,3198495,3323355,3323418,0E2f1incmplincmpl-1,-1,-1,2,1,2,
590NR_0739282448901+66296866427966427966427913662968,663080,663191,663311,663397,663486,663692,663800,663829,663933,664005,664035,664192,662986,663107,663284,663374,663450,663540,663788,663818,663920,663963,664024,664074,664279,0lncRNA:CR43652unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
594NM_1050082448883+124956612497971249566124979711249566,1249797,0F9N12.9; F9N12_9incmplincmpl0,
591NM_1196232448876-7932317939367932317939362793231,793471,793459,793936,0THY-2incmplincmpl0,0,
585NM_1206212448749-406541764065417614065,4176,0LAC12incmplincmpl0,
607NM_0010061942448902+288751828881732887518288817332887518,2887728,2887873,2887572,2887800,2888173,0COQ5incmplcmpl0,0,0,

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