Schema for refGene
  Database: bosTau3    Primary Table: refGene    Row Count: 14,971   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1000smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001014955varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr17varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 54435001int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 54448254int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 54435838int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 54447776int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 54435001,54441483,54447409,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 54435998,54441547,54448254,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 HSPB8varchar(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 cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        bosTau3.all_est.qName (via refGene.name)
      bosTau3.all_mrna.qName (via refGene.name)
      bosTau3.refFlat.name (via refGene.name)
      bosTau3.refSeqAli.qName (via refGene.name)
      bosTau3.xenoMrna.qName (via refGene.name)
      bosTau3.xenoRefGene.name (via refGene.name)
      bosTau3.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
1000NM_001014955chr17-54435001544482545443583854447776354435001,54441483,54447409,54435998,54441547,54448254,0HSPB8cmplcmpl2,1,0,
92NM_001014954chr10-200508362005873320051548200577511520050836,20051773,20052686,20053251,20053766,20054050,20054450,20054876,20055097,20055478,20055891,20056230,20056590,20057596,20 ...20051683,20051880,20052839,20053405,20053952,20054108,20054519,20054931,20055244,20055579,20055956,20056358,20056718,20057831,20 ...0DCAF11cmplcmpl0,1,1,0,0,2,2,1,1,2,0,1,2,0,-1,
614NM_001035107chr23+3801183390701938012823906509113801183,3814915,3815616,3824989,3840152,3844266,3847292,3849520,3852934,3889229,3906374,3801637,3814979,3815706,3825076,3840276,3844417,3847473,3849566,3853058,3889275,3907019,0TINAGcmplcmpl0,1,2,2,0,1,2,0,1,2,0,
609NM_001035106chr25+321626332228773216695322229833216263,3218354,3221867,3217103,3218565,3222877,0ZNF174cmplcmpl0,0,1,
885NM_001035096chr19-393377043943757439339298394373021639337704,39339192,39340773,39341985,39343702,39344868,39346541,39349091,39350508,39352214,39361157,39361698,39362964,39365933,39 ...39338010,39339406,39340986,39342042,39343747,39344929,39346672,39349166,39350635,39352310,39361226,39361793,39363039,39365988,39 ...0FBXL20cmplcmpl-1,0,0,0,0,2,0,0,2,2,2,0,0,2,0,0,
636NM_001035095chr25+668882367189436688856671763086688823,6697854,6700339,6701069,6704295,6704507,6708065,6717528,6688922,6697966,6700416,6701161,6704395,6704583,6708181,6718943,0PMM2cmplcmpl0,0,1,0,2,0,1,0,
713NM_001035105chr7-16825124168282481682650316828238316825124,16827274,16828120,16826636,16827440,16828248,0MRPL54cmplcmpl2,1,0,
119NM_001105003chr2+48302669486580934830266948658093848302669,48322423,48339029,48360632,48563507,48564835,48621253,48657992,48302738,48322485,48339117,48360722,48563606,48564965,48621376,48658093,0ARHGAP15incmplincmpl0,0,2,0,0,0,1,1,
722NM_001105001chr29-18002391180851951800239118076834718002391,18010269,18028468,18041103,18064355,18076689,18084986,18002499,18010411,18028532,18041245,18064477,18076854,18085195,0GAS2incmplcmpl0,2,1,0,1,0,-1,
732NM_001105001chr29+19269825192708601926982519270045119269825,19270860,0GAS2incmplcmpl2,

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