Schema for xenoRefGene
  Database: chrPic1    Primary Table: xenoRefGene    Row Count: 525,053   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 78smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001080327varchar(255) Name of gene (usually transcript_id from GTF)
chrom JH584520varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 6097682int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 6168649int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 6097682int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 6168649int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned Number of exons
exonStarts 6097682,6104701,6107949,610...longblob Exon start positions (or end positions for minus strand item)
exonEnds 6097769,6104806,6108060,610...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 EMC2varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,2,2,0,2,0,1,0,1,2,1,0,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
        chrPic1.all_mrna.qName (via xenoRefGene.name)
      chrPic1.xenoMrna.qName (via xenoRefGene.name)
      chrPic1.xenoRefFlat.name (via xenoRefGene.name)
      chrPic1.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
78NM_001080327JH584520-6097682616864960976826168649146097682,6104701,6107949,6109091,6111957,6112175,6136078,6145170,6150042,6150257,6153822,6153835,6155981,6168609,6097769,6104806,6108060,6109173,6112015,6112261,6136136,6145253,6150047,6150318,6153824,6153945,6155985,6168649,0EMC2cmplcmpl0,0,0,2,2,0,2,0,1,0,1,2,1,0,
601NM_001079882JH584847+2176975218500721770472185007132176975,2177469,2178032,2178868,2180424,2181143,2181305,2182047,2182509,2183071,2183814,2184198,2184929,2177089,2177553,2178180,2178912,2180472,2181167,2181359,2182118,2182619,2183203,2183912,2184463,2185007,0PRKD2cmplincmpl0,0,0,1,0,0,0,0,2,0,0,2,0,
589NM_001131240JH585051-5263195270805263195270804526319,526588,526696,526945,526382,526657,526909,527080,0ZNF23incmplincmpl0,0,0,0,
589NM_001131240JH585051-5263195270865263195270863526319,526588,526849,526388,526765,527086,0ZNF23incmplincmpl0,0,0,
624NM_001282904JH584722+518545052239705214791522388335185450,5214779,5223364,5185612,5215140,5223970,0OPRK1cmplcmpl-1,0,0,
600NM_001282894JH584449-208690720889682086907208896832086907,2088232,2088797,2086994,2088245,2088968,0casp3aincmplincmpl0,1,0,
606NM_001282894JH584623-280466128149212804661281492132804661,2809717,2814873,2804808,2809867,2814921,0casp3aincmplincmpl0,0,0,
594NM_001006567JH584795+121863912472581218669124724681218639,1224795,1225134,1232688,1236498,1240510,1244161,1247087,1218868,1225020,1225230,1232814,1236621,1240639,1244283,1247258,0OATcmplcmpl0,1,1,0,0,0,0,0,
585NM_001244010JH584475-62218106686622181066861062218,68343,69058,78404,78429,78554,87607,95461,97638,106397,62383,68431,69240,78408,78503,78944,87703,95547,97779,106686,0Slc20a2cmplcmpl0,2,0,2,0,0,0,1,1,0,
610NM_153615JH584612+336532033655483365320336554813365320,3365548,0RGL4incmplincmpl0,

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