Schema for xenoRefGene
  Database: xenTro1    Primary Table: xenoRefGene    Row Count: 582,134   Data last updated: 2020-09-02
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001076213varchar(255) Name of gene (usually transcript_id from GTF)
chrom scaffold_803varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 363637int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 433082int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 363637int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 433082int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 15int(10) unsigned Number of exons
exonStarts 363637,363756,363887,364580...longblob Exon start positions (or end positions for minus strand item)
exonEnds 363672,363803,363908,364696...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 ZNF45varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 1,2,2,0,2,0,0,0,0,1,2,0,1,0,0,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
        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)
      xenTro1.all_est.qName (via xenoRefGene.name)
      xenTro1.all_mrna.qName (via xenoRefGene.name)
      xenTro1.xenoRefFlat.name (via xenoRefGene.name)
      xenTro1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
73NM_001076213scaffold_803-36363743308236363743308215363637,363756,363887,364580,379028,379896,379949,380120,380333,415025,415192,415701,416000,416503,432950,363672,363803,363908,364696,379062,379928,379952,380249,380345,415027,415365,415748,416083,416573,433082,0ZNF45incmplincmpl1,2,2,0,2,0,0,0,0,1,2,0,1,0,0,
73NM_001076213scaffold_803-36460044184236460044184210364600,415207,415640,415721,416000,416225,432931,433025,433196,441719,364635,415433,415697,415748,416108,416302,433001,433082,433211,441842,0ZNF45incmplincmpl1,0,0,0,0,1,0,0,0,0,
74NM_001108230scaffold_49+1792927190000118053251899563181792927,1800084,1804723,1805316,1807244,1818662,1819345,1823487,1847671,1857958,1860959,1876666,1877915,1878043,1879709,1898608, ...1792984,1800172,1804806,1805461,1807379,1818790,1819500,1823581,1847776,1858129,1861056,1876821,1878003,1878046,1879915,1898866, ...0Agap1cmplincmpl-1,-1,-1,0,1,1,0,2,0,0,0,1,0,1,1,0,0,-1,
73NM_001273553scaffold_781+35798544958635798544958611357985,372962,398101,399530,399617,400584,424096,425252,446576,448049,449466,358132,373052,398230,399596,399656,400632,424195,425342,446648,448106,449586,0Ca-alpha1Dincmplincmpl0,0,0,0,0,0,0,0,0,0,0,
73NM_001273553scaffold_806-51787955748751787955748722517879,518051,518104,518309,520102,521239,521568,521824,522479,522633,530870,531639,532524,533101,536128,536349,549080,549603,55 ...517960,518054,518188,518414,520199,521367,521619,521912,522550,522735,530942,531795,532644,533224,536248,536430,549127,549736,55 ...0Ca-alpha1Dincmplincmpl0,0,0,0,2,0,0,2,0,0,0,0,0,0,0,0,1,0,0,0,0,0,
593NM_001106381scaffold_2+114463311572351144633115723571144633,1146392,1149505,1149887,1152155,1157085,1157208,1144705,1146484,1149767,1149968,1152224,1157181,1157235,0Susd2incmplincmpl0,0,2,0,0,0,0,
586NM_001195592scaffold_218+21846922192521846922192510218469,218885,219049,219095,219159,219882,220906,221234,221686,221859,218595,218957,219086,219157,219161,219949,220980,221347,221790,221925,0SRSF5cmplincmpl0,0,0,1,0,2,0,2,1,0,
590NM_001205602scaffold_169+74672276292774672276292717746722,748130,748333,748747,748886,749075,750376,750564,753604,754614,755089,755979,756920,757205,757295,757590,762798,746806,748270,748337,748821,748890,749180,750486,750640,753751,754698,755158,756136,757126,757262,757445,757710,762927,0SMPD4incmplincmpl0,0,2,0,2,0,0,2,0,0,0,0,1,0,0,0,0,
595NM_206234scaffold_108+137337713763451373377137634531373377,1374496,1376328,1373410,1374655,1376345,0nSybincmplincmpl0,0,0,
73NM_001087011scaffold_25+2947228170058170058170056294722,295399,426921,427103,498718,816957,294786,295405,426954,427107,499108,817005,0rap2c.Sunkunk-1,-1,-1,-1,-1,-1,

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