Schema for refFlat
  Database: galGal6    Primary Table: refFlat    Row Count: 7,356   Data last updated: 2018-10-26
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName DHRS4varchar(255) values Name of gene as it appears in genome browser.
name NM_001277125varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 68196int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 71610int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 68786int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 71608int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 68196,68998,69472,69891,700...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 68901,69054,69607,69943,701...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      galGal6.mrnaOrientInfo.name (via refFlat.name)
      galGal6.refGene.name (via refFlat.name)
      galGal6.refSeqAli.qName (via refFlat.name)
      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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
DHRS4NM_001277125chr1-68196716106878671608868196,68998,69472,69891,70046,70194,70829,71495,68901,69054,69607,69943,70117,70296,71007,71610,
CLC2DL3NM_001277858chr1+3014343031133014593025314301434,301833,302217,302413,301625,302015,302324,303113,
HCLS1NM_001031401chr1+35901937102636108137008015359019,361081,362418,362619,363613,364307,365953,366198,366599,367148,367428,368081,368561,369504,369943,359085,361165,362492,362749,363724,364362,366064,366309,366655,367218,367562,368189,368856,369576,371026,
RABL2BNM_001278112chr1+3876923916203877353912958387692,387918,388053,389090,389947,390516,390848,391214,387842,387948,388133,389170,390059,390614,390932,391620,
MIR6708NR_105579chr1+5722015723115723115723111572201,572311,
MIR1604NR_035090chr1+5968125969095969095969091596812,596909,
OPN1SWNM_205438chr1+7521247526157522687526152752124,752192,752147,752615,
ARF5NM_205325chr1-109601711028051096017110275951096017,1097907,1098187,1099866,1102692,1096143,1097979,1098297,1099947,1102805,
GCC1NM_001031589chr1+110322211081081103414110703521103222,1105727,1104461,1108108,
MIR1651NR_035142chr1+117846311785471178547117854711178463,1178547,

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