Schema for refFlat
  Database: oryCun2    Primary Table: refFlat    Row Count: 1,750   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LOC100008986varchar(255) values Name of gene as it appears in genome browser.
name NM_001082197varchar(255) values Name of gene
chrom chrUn0185varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 366227int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 371227int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 366283int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 370976int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 366227,367283,368603,370345...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 366475,367431,368874,370980...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)
      oryCun2.mrnaOrientInfo.name (via refFlat.name)
      oryCun2.refGene.name (via refFlat.name)
      oryCun2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LOC100008986NM_001082197chrUn0185-3662273712273662833709765366227,367283,368603,370345,371197,366475,367431,368874,370980,371227,
MIR302DNR_126585chr15+36770108367701763677017636770176136770108,36770176,
MIR302BNR_126582chr15+36769626367697063676970636769706136769626,36769706,
MIR191NR_126593chr9-16649736166498281664982816649828116649736,16649828,
MIR302ANR_126584chr15+36769945367700143677001436770014136769945,36770014,
MIR302CNR_126583chr15+36769769367698373676983736769837136769769,36769837,
LOC102723302NR_110379chr17+68749402687497006874970068749700168749402,68749700,
LOC102723302NR_110379chr17-68976224689765226897652268976522168976224,68976522,
LOC102723302NR_110379chr17-68986344689866426898664268986642168986344,68986642,
RN7SL1NR_037953chr17+68749402687497006874970068749700168749402,68749700,

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