Schema for refFlat
  Database: oviAri3    Primary Table: refFlat    Row Count: 1,022   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName HOXC6varchar(255) values Name of gene as it appears in genome browser.
name NM_001009335varchar(255) values Name of gene
chrom chr3varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 132338335int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 132340153int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 132338985int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 132340143int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 132338335,132339989,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 132339293,132340153,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)
      oviAri3.mrnaOrientInfo.name (via refFlat.name)
      oviAri3.refGene.name (via refFlat.name)
      oviAri3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
HOXC6NM_001009335chr3-1323383351323401531323389851323401432132338335,132339989,132339293,132340153,
POU1F1NM_001009350chr1-1540278681540435711540278681540435716154027868,154029100,154029909,154032527,154039693,154043429,154028078,154029161,154030074,154032752,154039765,154043571,
SLC11A1NM_001009345chr2+21937854021938946421937856321938905315219378540,219379180,219380341,219380774,219381964,219382474,219382882,219383431,219384203,219385712,219385909,219386440,21938819 ...219378639,219379314,219380464,219380894,219382071,219382545,219382950,219383587,219384362,219385802,219386029,219386590,21938826 ...
IL18NM_001009263chr15-21907864219324682190788421916805621907864,21910691,21911625,21915818,21916726,21932307,21908106,21910825,21911760,21915830,21916813,21932468,
IFNAR2NM_001009342chr1-1205505951205752851205512171205752468120550595,120556707,120564345,120565917,120568270,120570013,120571726,120575191,120551979,120556838,120564514,120566072,120568443,120570137,120571768,120575285,
CRHBPNM_001009339chr7+791004679220867910103792206167910046,7910662,7912189,7914091,7917865,7921903,7910184,7910816,7912404,7914240,7917983,7922086,
HNF4ANM_001205153chr13+723836417241355272383662724104581172383641,72387943,72389195,72395668,72396654,72400769,72401737,72404707,72409112,72410315,72410626,72383750,72388118,72389290,72395775,72396810,72400857,72401893,72404944,72409235,72410581,72413552,
RAP2ANM_001161878chr10+73983136740216417398313674021248373983136,74020922,74021212,73983430,74021124,74021641,
GPR50NM_001009726chrX-79755770797603117975577079760311279755770,79760124,79757311,79760311,
MTNR1ANM_001009725chr26-15118312151412141511840715141195215118312,15140963,15119276,15141214,

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