Schema for refGene
  Database: ce6    Primary Table: refGene    Row Count: 53,463   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 719smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001373633varchar(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 17616255int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 17619534int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 17616598int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 17619371int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 17616255,17617912,17618466,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 17616710,17618037,17618607,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ncs-7varchar(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 0,1,0,0,2,0,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
        ce6.all_est.qName (via refGene.name)
      ce6.all_mrna.qName (via refGene.name)
      ce6.mrnaOrientInfo.name (via refGene.name)
      ce6.refFlat.name (via refGene.name)
      ce6.refSeqAli.qName (via refGene.name)
      ce6.xenoMrna.qName (via refGene.name)
      ce6.xenoRefGene.name (via refGene.name)
      ce6.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
719NM_001373633chrX+17616255176195341761659817619371617616255,17617912,17618466,17618679,17618862,17619242,17616710,17618037,17618607,17618807,17618947,17619534,0ncs-7cmplcmpl0,1,0,0,2,0,
719NM_001373634chrX-17622623176407841762372817640656717622623,17624268,17624462,17625179,17626442,17627764,17640633,17623831,17624414,17624684,17625520,17626548,17627888,17640784,0H18N23.2cmplcmpl2,0,0,1,0,2,0,
719NM_171822chrX-17623728176281591762372817628159717623728,17624268,17624462,17625179,17626442,17627764,17628094,17623831,17624414,17624684,17625520,17626548,17627888,17628159,0H18N23.2cmplcmpl2,0,0,1,0,2,0,
719NM_001047826chrX+17649592176519901765009017651507317649592,17649897,17651227,17649638,17650191,17651990,0tmem-218cmplcmpl-1,0,2,
713NM_078323chrX+16860312168614381686031216861304416860312,16860581,16860725,16860987,16860528,16860676,16860940,16861438,0T20F7.3cmplcmpl0,0,2,1,
713NM_078324chrX-16865962168689481686631316868933816865962,16866650,16867344,16867502,16867962,16868263,16868406,16868834,16866445,16866890,16867456,16867675,16868147,16868358,16868642,16868948,0aakg-2cmplcmpl0,0,2,0,1,2,0,0,
713NM_078326chrX+168700711687826816872842168779591216870071,16871252,16873555,16873732,16874028,16874407,16875055,16875182,16875364,16876869,16877071,16877791,16870257,16873061,16873682,16873977,16874351,16874555,16875138,16875320,16875611,16877025,16877434,16878268,0T20F7.1cmplcmpl-1,0,0,1,0,2,0,2,2,0,0,0,
713NM_078327chrX-168779931688044316878064168803881116877993,16878218,16878623,16878885,16879042,16879187,16879387,16879606,16879843,16880111,16880307,16878171,16878372,16878833,16878992,16879131,16879270,16879562,16879800,16880046,16880202,16880443,0acs-9cmplcmpl1,0,0,1,2,0,2,0,1,0,0,
714NM_078350chrX-170217281703495117022185170301172317021728,17022376,17022500,17022901,17023363,17023807,17023988,17024174,17024434,17025047,17025426,17026163,17026548,17027052,17 ...17022327,17022453,17022596,17023011,17023760,17023938,17024067,17024363,17024650,17025254,17025602,17026384,17026670,17027333,17 ...0ptrn-1cmplcmpl2,0,0,1,0,1,0,0,0,0,1,2,0,1,2,1,2,0,0,0,0,0,-1,
714NM_001307917chrX-170217361703011717022185170301172217021736,17022376,17022500,17022901,17023363,17023807,17023988,17024174,17024434,17025047,17025426,17026163,17026548,17027052,17 ...17022327,17022453,17022596,17023011,17023760,17023938,17024067,17024363,17024650,17025254,17025602,17026390,17026670,17027333,17 ...0ptrn-1cmplcmpl2,0,0,1,0,1,0,0,0,0,1,2,0,1,2,1,2,0,0,0,0,0,

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