Schema for refFlat
  Database: rheMac2    Primary Table: refFlat    Row Count: 6,342   Data last updated: 2016-02-16
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName SPINLW1varchar(255) values Name of gene as it appears in genome browser.
name NM_001032841varchar(255) values Name of gene
chrom chr10varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 18896747int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 18901421int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 18896791int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 18901123int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 18896747,18897571,18900407,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 18896882,18897629,18900575,...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)
      rheMac2.refGene.name (via refFlat.name)
      rheMac2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
SPINLW1NM_001032841chr10+18896747189014211889679118901123418896747,18897571,18900407,18901112,18896882,18897629,18900575,18901421,
MIR218-1NR_032455chr5+15312110153122151531221515312215115312110,15312215,
MIR429NR_032520chr1+424184242419254241925424192514241842,4241925,
PRLNM_001047128chr4-22255920222713982225607522265452622255920,22258731,22261117,22262874,22265424,22271188,22256267,22258911,22261225,22263050,22265549,22271398,
NLRP3NM_001114351chr1-2095385412095656862095391482095655116209538541,209542955,209543643,209558625,209560871,209565228,209539248,209543126,209543815,209560375,209560991,209565686,
MIR190ANR_031990chr7+41206804412068894120688941206889141206804,41206889,
UTS2RNM_001032894chr16+77856904778580747785690477858074177856904,77858074,
MIR1911NR_128394chrX+1132711631132712221132712221132712221113271163,113271222,
NDFIP1NM_001194017chr6+1385268901385765981385270821385666529138526890,138527039,138552869,138553274,138557101,138559091,138562561,138566548,138573888,138526987,138527145,138552957,138553405,138557189,138559216,138562628,138566654,138576598,
C7H14orf79NM_001193779chr7+1683518871683604071683520341683596735168351887,168354187,168356708,168357863,168359511,168352457,168354333,168356838,168357980,168360407,

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