Schema for refGene
  Database: galGal3    Primary Table: refGene    Row Count: 7,422   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 976smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001037828varchar(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 51363875int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 51365483int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 51363882int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 51365388int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 51363875,51364206,51365074,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 51364012,51364404,51365483,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 TNFRSF13Cvarchar(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 0,1,1,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
        galGal3.all_est.qName (via refGene.name)
      galGal3.all_mrna.qName (via refGene.name)
      galGal3.mrnaOrientInfo.name (via refGene.name)
      galGal3.refFlat.name (via refGene.name)
      galGal3.refSeqAli.qName (via refGene.name)
      galGal3.xenoMrna.qName (via refGene.name)
      galGal3.xenoRefGene.name (via refGene.name)
      galGal3.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
976NM_001037828chr1+51363875513654835136388251365388351363875,51364206,51365074,51364012,51364404,51365483,0TNFRSF13Ccmplcmpl0,1,1,
651NM_001037827chr19+868379586902048683795869020468683795,8685002,8686033,8687028,8689393,8689776,8684495,8685066,8686217,8687244,8689438,8690204,0VEZF1incmplcmpl1,2,0,1,1,1,
586NM_001110841chr19-15706817210715769617210714157068,158388,158709,158985,159672,160209,160532,165529,165936,166378,167096,168142,168377,171811,158066,158516,158829,159098,159847,160283,161339,165610,166135,166423,167186,168225,168484,172107,0MLXIPLcmplcmpl2,0,0,1,0,1,1,1,0,0,0,1,2,0,
665NM_001001761chr10-10550607105719081055288610571775910550607,10558084,10560400,10561173,10562410,10566190,10567561,10570333,10571633,10553135,10558326,10560563,10561288,10562525,10566367,10567716,10570484,10571908,0CYP19A1cmplcmpl0,1,0,2,1,1,2,1,0,
11NM_001001760chr11+176904821817768417690514181771051317690482,17787697,17868495,17903664,17937001,17982990,18048791,18101367,18131720,18133003,18162720,18175735,18176866,17690559,17787809,17868704,17903781,17937154,17983135,18048970,18101508,18131903,18133257,18162863,18175969,18177684,0CDH13cmplcmpl0,0,1,0,0,0,1,0,0,0,2,1,1,
76NM_001001759chr6-4050309408379240506384083684174050309,4056512,4057686,4060233,4061376,4064086,4067411,4068848,4071034,4072318,4073978,4075480,4076000,4077405,4078295,4082801, ...4051190,4056767,4057915,4060301,4061541,4064239,4067615,4068949,4071113,4072462,4074095,4075567,4076090,4077456,4078441,4082897, ...0CDHR1cmplcmpl0,0,2,0,0,0,0,1,0,0,0,0,0,0,1,1,0,
11NM_001257313chr4+20955847209950592095593320994900820955847,20956505,20957314,20959166,20972195,20973988,20993979,20994793,20955936,20956571,20957372,20959315,20972270,20974103,20994024,20995059,0MND1cmplcmpl0,0,0,1,0,0,1,1,
88NM_001257299chr2-164075471658880716407547165888071116407547,16409726,16411976,16415759,16427624,16456358,16487814,16507807,16512628,16575802,16588059,16408990,16409873,16412082,16415898,16427863,16456468,16487883,16508025,16512731,16575908,16588807,0GPR158cmplincmpl0,0,2,1,2,0,0,1,0,2,1,
617NM_001257298chr26+421802842380674218115423790054218028,4228598,4236342,4237037,4237730,4218214,4228709,4236387,4237122,4238067,0NUDT3cmplcmpl0,0,0,0,1,
617NM_001257297chr26+420989142161774210861421613464209891,4210861,4211390,4214923,4215548,4216092,4209944,4211011,4211562,4215001,4215604,4216177,0RPS10cmplcmpl-1,0,0,1,1,0,

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