Schema for refGene
  Database: criGri1    Primary Table: refGene    Row Count: 555   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001244032varchar(255) values Name of gene (usually transcript_id from GTF)
chrom KE376447varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 130628int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 155912int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 130703int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 155912int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 130628,131270,134260,139891...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 131236,131409,134373,139923...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Ercc4varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('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 1,1,2,0,2,1,1,1,0,2,2,1,1,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
        criGri1.all_est.qName (via refGene.name)
      criGri1.all_mrna.qName (via refGene.name)
      criGri1.mrnaOrientInfo.name (via refGene.name)
      criGri1.refFlat.name (via refGene.name)
      criGri1.refSeqAli.qName (via refGene.name)
      criGri1.xenoMrna.qName (via refGene.name)
      criGri1.xenoRefGene.name (via refGene.name)
      criGri1.xenoRefSeqAli.qName (via refGene.name)
      hgFixed.gbCdnaInfo.acc (via refGene.name)
      hgFixed.gbMiscDiff.acc (via refGene.name)
      hgFixed.gbSeq.acc (via refGene.name)
      hgFixed.gbWarn.acc (via refGene.name)
      hgFixed.imageClone.acc (via refGene.name)
      hgFixed.refLink.mrnaAcc (via refGene.name)
      hgFixed.refSeqStatus.mrnaAcc (via refGene.name)
      hgFixed.refSeqSummary.mrnaAcc (via refGene.name)
      knownGeneV39.kgXref.refseq (via refGene.name)
      knownGeneV39.knownToRefSeq.value (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
73NM_001244032KE376447-13062815591213070315591213130628,131270,134260,139891,139958,141926,143562,144652,145455,147388,148426,148465,155729,131236,131409,134373,139923,139983,142524,143673,144772,145636,147596,148465,148616,155912,0Ercc4cmplincmpl1,1,2,0,2,1,1,1,0,2,2,1,1,
585NM_001244047KE379418-30289333453058033345430289,31102,32138,33246,30797,31248,32273,33345,0Xbp1cmplincmpl2,0,0,0,
609NM_001244854KE381181-320434532056223204537320555033204345,3204972,3205499,3204960,3205490,3205622,0Gapdhcmplcmpl0,0,0,
588NM_001244853KE383444+43065549573443073149532810430655,432210,433464,445586,446056,457117,458677,461187,483527,495259,430742,432269,433615,445664,446165,457224,458791,461243,483627,495734,0Pex7cmplcmpl0,0,2,0,0,1,0,0,2,0,
73NM_001244852KE380114+78435979892078435979892012784359,785898,787927,789458,790372,792536,793853,794948,795781,796557,798013,798821,784385,786109,788080,789569,790501,792656,793970,795076,795908,796725,798166,798920,0Smu1cmplcmpl0,2,0,0,0,0,0,0,2,0,0,0,
585NM_001244851KE383522-39731487594087542689439731,41102,42517,48654,40940,41258,42691,48759,0Pea15cmplcmpl1,1,0,-1,
599NM_001244849KE376951-1888984189604818891171895882101888984,1890066,1890455,1890671,1892564,1892812,1893170,1894658,1895482,1895787,1889279,1890262,1890582,1890791,1892684,1892929,1893293,1894865,1895532,1896048,0Efemp2cmplcmpl0,2,1,1,1,1,1,1,2,0,
9NM_001244850KE379574-8405661238556841256119661111840566,866281,909632,923282,968677,1048174,1053580,1119643,1184727,1196555,1238457,841381,866368,909747,923318,968848,1048283,1053753,1119722,1184781,1196630,1238556,0Adkcmplcmpl1,1,0,0,0,2,0,2,2,0,-1,
586NM_001246829KE382569-2230202295972236862295978223020,223987,224325,224768,225950,226801,228057,229474,223764,224128,224418,224863,226068,226906,228269,229597,0Hspa9cmplincmpl0,0,0,1,0,0,1,2,
74NM_001246828KE381095-1364105148803913641051488039251364105,1365745,1377307,1389195,1402947,1405201,1419614,1422674,1431795,1433536,1434622,1443308,1444906,1446755,1454272,1462711, ...1364330,1365863,1377461,1389330,1402997,1405315,1419703,1422785,1431909,1433655,1434751,1443522,1445107,1446866,1454354,1462795, ...0Pld1cmplcmpl0,2,1,1,2,2,0,0,0,1,1,0,0,0,2,2,2,2,2,0,0,2,0,1,0,

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