Schema for refGene
  Database: panPan2    Primary Table: refGene    Row Count: 218   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 1smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001293718varchar(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 33550139int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 33589402int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 33551275int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 33589052int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 33550139,33550413,33550626,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 33550320,33550534,33550838,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 AZIN2varchar(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,-1,-1,0,0,0,2,2,0,1,0,2,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)
      panPan2.all_mrna.qName (via refGene.name)
      panPan2.mrnaOrientInfo.name (via refGene.name)
      panPan2.refFlat.name (via refGene.name)
      panPan2.refSeqAli.qName (via refGene.name)
      panPan2.xenoRefGene.name (via refGene.name)
      panPan2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1NM_001293718chr1+335501393358940233551275335890521233550139,33550413,33550626,33551203,33552970,33561068,33562300,33563556,33565713,33567073,33586771,33588913,33550320,33550534,33550838,33551380,33553144,33561241,33562435,33563722,33565876,33567186,33586986,33589402,0AZIN2cmplcmpl-1,-1,-1,0,0,0,2,2,0,1,0,2,
1507NR_106555chr11-1209120971209121771209121771209121771120912097,120912177,0MIR100unkunk-1,
876NR_106545chr3+38151349381514263815142638151426138151349,38151426,0MIR26Aunkunk-1,
1433NR_106586chr1+1112041261112042011112042011112042011111204126,111204201,0MIR197unkunk-1,
1582NM_001290340chr1+1307650021307739741307652891307738595130765002,130769316,130770210,130772811,130773716,130765321,130769453,130770386,130772897,130773974,0OAZ3cmplcmpl0,2,1,0,2,
1582NM_001301415chr1+1307688081307739741307688751307738595130768808,130769316,130770210,130772811,130773716,130769042,130769453,130770386,130772897,130773974,0OAZ3cmplcmpl0,2,1,0,2,
1647NM_001302655chr1-1392241381392266141392241381392266144139224138,139224739,139225779,139226568,139224344,139225008,139226125,139226614,0SLAMF9cmplcmpl1,2,1,0,
874NM_001279181chr2A-378979323794023837897932379402381537897932,37898133,37899852,37905357,37910575,37912360,37916482,37927491,37928994,37930287,37930526,37931651,37933569,37939283,37 ...37898055,37898190,37899954,37905486,37910756,37912519,37916605,37927554,37929029,37930381,37930603,37931778,37933718,37939404,37 ...0EIF2AK2cmplcmpl0,0,0,0,2,2,2,2,0,2,0,2,0,2,0,
1739NR_106578chr1-1513465541513466641513466641513466641151346554,151346664,0MIR214unkunk-1,
2033NR_106577chr1+1898126561898127661898127661898127661189812656,189812766,0MIR205unkunk-1,

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