Schema for refGene
  Database: dm1    Primary Table: refGene    Row Count: 34,386   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 631smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001382104varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr3Rvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 6110329int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 6128638int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 6116986int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 6128039int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 14int(10) unsigned range Number of exons
exonStarts 6110329,6116839,6117312,611...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 6110452,6117192,6117512,611...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Nuak1varchar(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 -1,0,2,1,0,1,1,1,2,2,2,0,2,1,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
        dm1.all_est.qName (via refGene.name)
      dm1.all_mrna.qName (via refGene.name)
      dm1.bdgpToRefSeq.value (via refGene.name)
      dm1.mrnaOrientInfo.name (via refGene.name)
      dm1.refFlat.name (via refGene.name)
      dm1.refSeqAli.qName (via refGene.name)
      dm1.xenoMrna.qName (via refGene.name)
      dm1.xenoRefGene.name (via refGene.name)
      dm1.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
631NM_001382104chr3R+6110329612863861169866128039146110329,6116839,6117312,6117576,6117855,6118933,6121060,6122473,6123179,6123508,6123985,6124188,6125373,6127683,6110452,6117192,6117512,6117794,6118453,6120058,6121801,6122849,6123437,6123637,6124115,6124331,6125492,6128638,0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,1,
624NM_001382200chr3R-519334051960995193978519591675193340,5194193,5194436,5194634,5194792,5195073,5195790,5194130,5194376,5194565,5194721,5195006,5195448,5196099,0FERcmplcmpl1,1,1,1,0,0,0,
627NM_001382202chr3R-562350656267645624176562646825623506,5626406,5626328,5626764,0CG9467cmplcmpl2,0,
627NM_001382203chr3R-562350656267645624026562646825623506,5626406,5626328,5626764,0CG9467cmplcmpl2,0,
78NM_001382173chr3R+570041858146165700878570108875700418,5756101,5769218,5769414,5808018,5812387,5812636,5701961,5756283,5769325,5769632,5808110,5812573,5814616,0CG46467cmplcmpl0,-1,-1,-1,-1,-1,-1,
631NM_001382099chr3R+6090045612863861169866128039136090045,6116839,6117312,6117576,6117855,6118933,6122473,6123179,6123508,6123985,6124188,6125373,6127683,6090618,6117192,6117512,6117794,6118453,6120058,6122849,6123437,6123637,6124115,6124331,6125492,6128638,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,
631NM_001382103chr3R+6090045612863861169866128039156090045,6116839,6117312,6117576,6117855,6118933,6121060,6122473,6123179,6123508,6123985,6124188,6124741,6125373,6127683,6090618,6117192,6117512,6117794,6118453,6120058,6121801,6122849,6123437,6123637,6124115,6124331,6124798,6125492,6128638,0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,2,1,
631NM_001382098chr3R+6090045613420761169866133460146090045,6116839,6117312,6117576,6117855,6118933,6122473,6123179,6123508,6123985,6124188,6125373,6129049,6133162,6090618,6117192,6117512,6117794,6118453,6120058,6122849,6123437,6123637,6124115,6124331,6125492,6133106,6134207,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,2,
631NM_001382101chr3R+6090045613420761169866133217166090045,6116839,6117312,6117576,6117855,6118933,6121060,6122473,6123179,6123508,6123985,6124188,6124741,6125373,6129049,6133162,6090618,6117192,6117512,6117794,6118453,6120058,6121801,6122849,6123437,6123637,6124115,6124331,6124798,6125492,6133106,6134207,0Nuak1cmplcmpl-1,0,2,1,0,1,1,1,2,2,2,0,2,2,1,2,
631NM_001382102chr3R+6090045613420761169866133217146090045,6116839,6117312,6117576,6117855,6118933,6122473,6123179,6123508,6123985,6124188,6125373,6129049,6133162,6090618,6117192,6117512,6117794,6118453,6120058,6122849,6123437,6123637,6124115,6124331,6125492,6133106,6134207,0Nuak1cmplcmpl-1,0,2,1,0,1,1,2,2,2,0,2,1,2,

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