Schema for refFlat
  Database: taeGut2    Primary Table: refFlat    Row Count: 1,263   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LOC100190510varchar(255) values Name of gene as it appears in genome browser.
name NM_001245268varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 2322980int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 2381582int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 2323027int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 2380903int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 2322980,2340930,2380775,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 2323036,2340982,2381582,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)
      taeGut2.mrnaOrientInfo.name (via refFlat.name)
      taeGut2.refGene.name (via refFlat.name)
      taeGut2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LOC100190510NM_001245268chr1+232298023815822323027238090332322980,2340930,2380775,2323036,2340982,2381582,
PSMA5NM_001198816chr26-171510717229381715304172293871715107,1718852,1719932,1720716,1720721,1720855,1722808,1715382,1718939,1720035,1720720,1720776,1720966,1722938,
MIRLET7C-1NR_049035chr1+1096626811096627731096627731096627731109662681,109662773,
MIRLET7C-1NR_049035chrUn_ABQF01102820+253826302630263012538,2630,
CWC25NM_001245143chr27+308446430956573084464309516383084464,3090535,3091091,3091415,3092025,3092546,3094074,3095042,3084510,3090592,3091216,3091485,3092153,3092633,3094236,3095657,
TM2D2NM_001245142chr22-297662429771132977113297711312976624,2977113,
MIR10ANR_049164chr7+17079280170793921707939217079392117079280,17079392,
MIR34C-1NR_049160chr24-175271017527871752787175278711752710,1752787,
JMJD8NM_001159400chr14+1412150171608114121501715938131412150,1412165,1412171,1712680,1714189,1714307,1714649,1714788,1714969,1715106,1715435,1715652,1715857,1412165,1412170,1412176,1712695,1714228,1714392,1714698,1714885,1715038,1715226,1715503,1715787,1716081,
RHOBTB3NM_001198813chrZ-217388932176243621738893217624361121738893,21740603,21741762,21743104,21745878,21747546,21749960,21751114,21752041,21754052,21762219,21739009,21740700,21741929,21743278,21745990,21747659,21750329,21751226,21752193,21754245,21762436,

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