Schema for refFlat
  Database: aptMan1    Primary Table: refFlat    Row Count: 1   Data last updated: 2020-05-05
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName TBX5varchar(255) values Name of gene as it appears in genome browser.
name NM_001315498varchar(255) values Name of gene
chrom NW_013989391v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 205389int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 252760int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 205389int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 252760int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 205389,210620,213814,214713...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 205536,210715,213934,214861...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      aptMan1.mrnaOrientInfo.name (via refFlat.name)
      aptMan1.refGene.name (via refFlat.name)
      aptMan1.refSeqAli.qName (via refFlat.name)
      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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
TBX5NM_001315498NW_013989391v1+2053892527602053892527608205389,210620,213814,214713,219284,232189,242642,252176,205536,210715,213934,214861,219437,232281,242869,252760,

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