Schema for refGene
  Database: papAnu2    Primary Table: refGene    Row Count: 509   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1548smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001112637varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr2varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 126224396int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 126230902int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 126224407int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 126230890int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 126224396,126226114,1262263...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 126224563,126226258,1262263...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 IL12Avarchar(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 0,0,0,0,0,1,0,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
        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)
      papAnu2.all_est.qName (via refGene.name)
      papAnu2.all_mrna.qName (via refGene.name)
      papAnu2.mrnaOrientInfo.name (via refGene.name)
      papAnu2.refFlat.name (via refGene.name)
      papAnu2.refSeqAli.qName (via refGene.name)
      papAnu2.xenoMrna.qName (via refGene.name)
      papAnu2.xenoRefGene.name (via refGene.name)
      papAnu2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1548NM_001112637chr2-1262243961262309021262244071262308907126224396,126226114,126226349,126226466,126226830,126229629,126230772,126224563,126226258,126226391,126226508,126226944,126229775,126230902,0IL12Acmplcmpl0,0,0,0,0,1,0,
1505NM_001164588chr7-1206141741206683111206141741206683118120614174,120616003,120630525,120638094,120641629,120650428,120664345,120667949,120614361,120616184,120630659,120638233,120641929,120650545,120664518,120668311,0ESR2cmplcmpl2,1,2,1,1,1,2,0,
586NM_001279520JH684887+1468481498691468481498698146848,147050,147561,148702,149080,149642,149817,149865,146921,147320,147837,148978,149197,149675,149865,149869,0LOC101007932cmplcmpl0,1,1,1,1,1,1,2,
1545NM_001168755chr6+12587621312592539312587621312592539310125876213,125894312,125895763,125904622,125909746,125913726,125916987,125918083,125922095,125925317,125876606,125894416,125895918,125904794,125909873,125913821,125917202,125918266,125922231,125925393,0SLC22A4cmplcmpl0,0,2,1,2,0,2,1,1,2,
1665NM_001168797chrX+1416313681416413041416313681416413044141631368,141636511,141639502,141641136,141631480,141636808,141639671,141641304,0OPN1LWcmplincmpl0,1,1,2,
1667NM_001168807chrX-1418559201418645471418559201418645479141855920,141856317,141856520,141856932,141857407,141857586,141860696,141861628,141864534,141856016,141856444,141856605,141856983,141857466,141857710,141860720,141861742,141864547,0FAM3Acmplcmpl0,2,1,1,2,1,1,1,0,
1667NM_001168806chrX-1418400061418414371418400061418414374141840006,141841388,141841395,141841421,141841388,141841395,141841421,141841437,0SLC10A3cmplcmpl1,2,2,0,
1664NM_001168796chrX+1414573211414581071414573211414581071141457321,141458107,0TMEM187cmplcmpl0,
1666NM_001168805chrX+14178932114179350714178932114179350710141789321,141789561,141789802,141790743,141791209,141791934,141792458,141792946,141793209,141793354,141789429,141789661,141789937,141790942,141791341,141792034,141792630,141793091,141793264,141793507,0GDI1incmplcmpl0,0,1,1,2,2,0,1,2,0,
207NM_001168795chrX-14142350314144543014142350314144543026141423503,141423725,141424424,141424983,141425520,141425753,141426005,141426646,141428065,141428524,141430649,141431080,14143137 ...141423543,141423789,141424725,141425169,141425658,141425872,141426323,141427091,141428229,141430001,141430870,141431219,14143151 ...0HCFC1cmplcmpl2,1,0,0,0,1,1,0,1,0,1,0,1,0,0,0,0,1,1,1,2,1,2,0,1,0,

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