Schema for refFlat
  Database: loxAfr3    Primary Table: refFlat    Row Count: 23   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 CCR5varchar(255) values Name of gene as it appears in genome browser.
name NM_001280878varchar(255) values Name of gene
chrom scaffold_12varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 21135801int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 21137050int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 21135887int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 21136949int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 21135801,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 21137050,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)
      loxAfr3.mrnaOrientInfo.name (via refFlat.name)
      loxAfr3.refGene.name (via refFlat.name)
      loxAfr3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
CCR5NM_001280878scaffold_12-21135801211370502113588721136949121135801,21137050,
HBB/DNM_001280882scaffold_116-248741824887622487435248873632487418,2488293,2488644,2487564,2488516,2488762,
OPN1LWNM_001280862scaffold_120-187303318845181873033188449251873033,1874265,1876074,1878658,1884380,1873273,1874431,1876243,1878955,1884518,
RHONM_001280858scaffold_12-33702277337085273370298733708435533702277,33703914,33704283,33705763,33708074,33703098,33704154,33704449,33705932,33708527,
OPN1SWNM_001280859scaffold_5-98283900982879639828458398287956598283900,98285911,98286572,98287096,98287598,98284703,98286151,98286738,98287265,98287963,
INSL5NM_001280873scaffold_17+27152479271575172715247927157517327152479,27154107,27157284,27152582,27154227,27157517,
ADI1NM_001286027scaffold_20-12372175123894581237217512389458412372175,12374982,12380710,12389338,12372295,12375162,12380830,12389458,
RNASEH1NM_001286025scaffold_20-12430957124426201243102912442538812430957,12432106,12433803,12434384,12435715,12437996,12441224,12442407,12431116,12432231,12433888,12434439,12435815,12438161,12441340,12442620,
RPS7NM_001286026scaffold_20+12454862124619511245486512461951612454862,12455230,12456338,12456934,12461132,12461873,12454940,12455302,12456482,12456999,12461283,12461951,
LOC100665288NM_001303260scaffold_3-260990732616531026099073261653103526099073,26102560,26103534,26106400,26106659,26107321,26108415,26110707,26113071,26115609,26117455,26117825,26118211,26119718,26 ...26099127,26102728,26103720,26106472,26106774,26107374,26108490,26110836,26113167,26115837,26117647,26117912,26118299,26119852,26 ...

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