Schema for refGene
  Database: panPan1    Primary Table: refGene    Row Count: 117   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 593smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001279200varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JH650433varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1114115int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1115261int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1114115int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1115261int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1114115,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1115261,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 GPR34varchar(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,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)
      panPan1.all_mrna.qName (via refGene.name)
      panPan1.mrnaOrientInfo.name (via refGene.name)
      panPan1.refFlat.name (via refGene.name)
      panPan1.refSeqAli.qName (via refGene.name)
      panPan1.xenoRefGene.name (via refGene.name)
      panPan1.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
593NM_001279200JH650433-111411511152611114115111526111114115,1115261,0GPR34cmplcmpl0,
669NR_106557JH650376+11122419111225001112250011122500111122419,11122500,0MIR29B-1unkunk-1,
604NR_106554JH650491+252212125222022522202252220212522121,2522202,0MIR99Aunkunk-1,
610NR_106608JH650406-340179034018713401871340187113401790,3401871,0MIR106Aunkunk-1,
664NR_106596JH650624+10418657104187391041873910418739110418657,10418739,0MIR19Aunkunk-1,
678NR_106606JH650376+12222961122230711222307112223071112222961,12223071,0MIR183unkunk-1,
601NM_001279229JH650283+212116121307412121161213074162121161,2122166,2127707,2129143,2129444,2130370,2121257,2122346,2127896,2129320,2129586,2130741,0AIPL1cmplcmpl0,0,0,0,0,1,
599NR_106579JH650607-186040118605111860511186051111860401,1860511,0MIR216unkunk-1,
657NM_001291493JH650518-9504614954326995068799521921139504614,9507580,9508130,9511347,9512471,9512948,9514532,9517019,9517925,9521819,9528664,9536921,9542794,9506991,9507795,9508246,9511510,9512546,9513030,9514667,9517192,9518099,9522016,9528810,9537059,9543269,0AZIN1cmplcmpl2,0,1,0,0,2,2,0,0,0,-1,-1,-1,
625NM_001304546JH650268+534361353531545351152535276925343613,5350925,5344147,5353154,0ERVW-1cmplcmpl-1,0,

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