Schema for refGene
  Database: melGal5    Primary Table: refGene    Row Count: 109   Data last updated: 2017-01-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 885smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001303146varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 39385517int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 39386204int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 39385517int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 39386204int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 39385517,39385755,39385764,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 39385754,39385763,39385787,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MYF6varchar(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 0,0,2,2,2,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 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)
      melGal5.all_est.qName (via refGene.name)
      melGal5.all_mrna.qName (via refGene.name)
      melGal5.mrnaOrientInfo.name (via refGene.name)
      melGal5.refFlat.name (via refGene.name)
      melGal5.refSeqAli.qName (via refGene.name)
      melGal5.xenoRefGene.name (via refGene.name)
      melGal5.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
885NM_001303146chr1+39385517393862043938551739386204539385517,39385755,39385764,39385787,39386080,39385754,39385763,39385787,39385898,39386204,0MYF6cmplcmpl0,0,2,2,2,
1006NM_001303149chr1+55186408551949695518640855194949255186408,55194889,55186590,55194969,0LOC678666incmplcmpl1,0,
1006NM_001303149chr1+55221571552262095522171555226209255221571,55226047,55221778,55226209,0LOC678666cmplincmpl0,0,
136NM_001303223chr1+66841084668617866684109966861572466841084,66847308,66849720,66861455,66841210,66847487,66849880,66861786,0KRAScmplcmpl0,0,2,0,
1161NM_001303196chr1+755882127559942275593919755992611075588212,75593848,75595535,75595794,75596110,75596805,75597281,75597610,75597976,75599245,75588282,75593980,75595709,75595938,75596386,75597168,75597524,75597729,75598044,75599422,0CD4cmplcmpl-1,0,1,1,1,1,1,1,0,2,
1163NM_001303179chr1+758006887580461275801123758043861275800688,75801105,75801774,75802155,75802346,75802611,75802810,75803050,75803341,75803641,75803867,75804316,75800727,75801146,75801874,75802262,75802437,75802727,75802892,75803202,75803420,75803725,75803965,75804612,0GAPDHcmplcmpl-1,0,2,0,2,0,2,0,2,0,0,2,
1303NM_001303222chr1+94118968941286579411905194128602694118968,94120401,94121835,94124191,94125775,94128388,94119235,94120515,94122081,94124356,94125836,94128657,0POU1F1cmplcmpl0,1,1,1,1,2,
1658NM_001303166chr1+14072515114074935214072521414074866523140725151,140727745,140730905,140731077,140732566,140732860,140733198,140734465,140735995,140737139,140737845,140739901,14074003 ...140725218,140727777,140730990,140731219,140732686,140732960,140733289,140734549,140736078,140737226,140737935,140739946,14074007 ...0SLC15A1cmplcmpl0,1,0,1,2,2,0,1,1,0,0,0,0,0,2,0,0,0,2,2,0,0,0,
2034NM_001303164chr1-1899630271899664491899633871899661966189963027,189963604,189963861,189964987,189965735,189966070,189963493,189963785,189963963,189965185,189965946,189966449,0LOC100303663cmplcmpl2,1,1,1,0,0,
701NM_001309275chr10+15230401152493291523041515248485515230401,15232060,15239296,15246324,15248353,15230484,15232228,15239360,15246374,15249329,0SELENOFcmplcmpl0,0,0,1,0,

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