Schema for refGene
  Database: ce4    Primary Table: refGene    Row Count: 51,604   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 709smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NR_166952varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 16332356int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 16335019int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 16335019int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 16335019int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 16332356,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 16335019,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 C11G6.7varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -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
        ce4.all_est.qName (via refGene.name)
      ce4.all_mrna.qName (via refGene.name)
      ce4.mrnaOrientInfo.name (via refGene.name)
      ce4.refFlat.name (via refGene.name)
      ce4.refSeqAli.qName (via refGene.name)
      ce4.xenoMrna.qName (via refGene.name)
      ce4.xenoRefGene.name (via refGene.name)
      ce4.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
709NR_166952chrX+16332356163350191633501916335019116332356,16335019,0C11G6.7unkunk-1,
709NM_001270344chrX+16340808163455031634080816345503416340808,16342201,16343970,16345349,16341015,16342395,16344462,16345503,0taf-3cmplcmpl0,0,2,2,
709NM_001381177chrX-162547561626210016254928162600351116254756,16256645,16257371,16257668,16257866,16258052,16258827,16258968,16259152,16259975,16261944,16255020,16256952,16257591,16257781,16257998,16258194,16258911,16259105,16259227,16260043,16262100,0sgk-1cmplcmpl1,0,2,0,0,2,2,0,0,0,-1,
709NM_001047834chrX-162549281626196616254928162619661116254928,16256645,16257371,16257668,16257866,16258052,16258827,16258968,16259152,16259975,16261944,16255020,16256952,16257591,16257781,16257998,16258194,16258911,16259105,16259227,16260043,16261966,0sgk-1cmplcmpl1,0,2,0,0,2,2,0,0,1,0,
709NM_078248chrX-16267111162699841626740816269966616267111,16267506,16268009,16268394,16269191,16269490,16267459,16267623,16268171,16269147,16269378,16269984,0ifa-3cmplcmpl0,0,0,0,2,0,
709NM_001373609chrX+162756771628244616275687162822151416275677,16275922,16276598,16276875,16277224,16277781,16278152,16278548,16279066,16279942,16280103,16280571,16281845,16282027,16275761,16276155,16276834,16277171,16277555,16277964,16278391,16278934,16279200,16280005,16280343,16281447,16281978,16282446,0sdc-1cmplcmpl0,2,1,0,2,0,0,2,1,0,0,0,0,1,
709NM_001313381chrX-16285513162929491628603716292887416285513,16286530,16291996,16292812,16286095,16286697,16292161,16292949,0F52E10.4cmplcmpl2,0,0,0,
709NM_001313421chrX-16286037162860941628603716286094116286037,16286094,0F52E10.4cmplcmpl0,
709NM_078252chrX-16286037162866731628603716286673216286037,16286530,16286095,16286673,0F52E10.4cmplcmpl2,0,
709NM_001313382chrX-16286037162920681628603716292068316286037,16286530,16291996,16286095,16286697,16292068,0F52E10.4cmplcmpl2,0,0,

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