Schema for refFlat
  Database: susScr11    Primary Table: refFlat    Row Count: 4,614   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MIR9821varchar(255) values Name of gene as it appears in genome browser.
name NR_128506varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1340182int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1340263int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1340263int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1340263int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1340182,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1340263,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      hgFixed.gbCdnaInfo.acc (via refFlat.name)
      hgFixed.gbSeq.acc (via refFlat.name)
      hgFixed.imageClone.acc (via refFlat.name)
      hgFixed.refLink.mrnaAcc (via refFlat.name)
      hgFixed.refSeqStatus.mrnaAcc (via refFlat.name)
      hgFixed.refSeqSummary.mrnaAcc (via refFlat.name)
      knownGeneV39.kgXref.refseq (via refFlat.name)
      knownGeneV39.knownToRefSeq.value (via refFlat.name)
      susScr11.mrnaOrientInfo.name (via refFlat.name)
      susScr11.refGene.name (via refFlat.name)
      susScr11.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIR9821NR_128506chr1-134018213402631340263134026311340182,1340263,
HYAL1NM_214441chr13-32798134328007053279838332800155332798134,32798874,32799255,32798701,32798964,32800705,
HYAL3NM_214439chr13-32791264327928443279126432792827332791264,32791639,32791933,32791540,32791729,32792844,
HYAL2NM_214440chr13-32805496328078713280552332807867432805496,32805541,32806335,32806937,32805534,32805934,32806425,32807871,
SLC30A8NM_001367266chr4-21517485215551152151763721555115921517485,21519063,21524503,21526222,21531120,21531261,21532655,21542867,21555044,21517783,21519198,21524609,21526373,21531261,21531273,21532802,21543067,21555115,
CREB1NM_001361427chr15+1107055501107730371107270801107669509110705550,110727072,110733498,110735087,110742596,110747948,110755271,110757482,110766805,110705776,110727194,110733645,110735129,110742697,110748091,110755454,110757633,110773037,
MSL3NM_001359942chrX+8519398853524985195208534541148519398,8520449,8520866,8521320,8521758,8522532,8523459,8524139,8525101,8527075,8527977,8530818,8531501,8534441,8519528,8520585,8520949,8521416,8521859,8522618,8523582,8524300,8525260,8527338,8528087,8530918,8531586,8535249,
PRXL2ANM_001359936chr14+82249451822712278226192482270583782249451,82250208,82261906,82263847,82266583,82267307,82270469,82249653,82250322,82262069,82263939,82266724,82267472,82271227,
MSL3NM_001359944chrX+8520688853524985234928534541118520688,8521758,8522532,8523459,8524139,8525101,8527075,8527977,8530818,8531501,8534441,8520949,8521859,8522618,8523582,8524300,8525260,8527338,8528087,8530918,8531586,8535249,
MSL3NM_001359943chrX+8519398853524985194268534541148519398,8520449,8520866,8521320,8521758,8522532,8523459,8524139,8525101,8527075,8527977,8530818,8531501,8534441,8519599,8520585,8520949,8521416,8521859,8522618,8523582,8524300,8525260,8527338,8528087,8530918,8531586,8535249,

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