Schema for refFlat
  Database: monDom4    Primary Table: refFlat    Row Count: 1,242   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 VN2R619varchar(255) values Name of gene as it appears in genome browser.
name NM_001099571varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 296506788int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 296533452int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 296506788int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 296533452int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned range Number of exons
exonStarts 296506788,296510734,2965122...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 296507693,296510858,2965124...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)
      monDom4.mrnaOrientInfo.name (via refFlat.name)
      monDom4.refGene.name (via refFlat.name)
      monDom4.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
VN2R619NM_001099571chr5-2965067882965334522965067882965334526296506788,296510734,296512226,296526231,296529290,296533207,296507693,296510858,296512445,296527035,296529582,296533452,
MIR7385I-2NR_162978chrX+460905346091154609115460911514609053,4609115,
CASP18NM_001114360chr7+1585604201586100851585604201586100858158560420,158590367,158593267,158596069,158601120,158606091,158607762,158609940,158560713,158590473,158593409,158596135,158601188,158606203,158608246,158610085,
MIR7385HNR_162979chrX+461542046154794615479461547914615420,4615479,
MIR7385I-1NR_162980chrX+461678746168464616846461684614616787,4616846,
MIR7385G-3NR_162981chrX+461777646178364617836461783614617776,4617836,
MIR12401NR_162982chrX-809549180955538095553809555318095491,8095553,
MIRLET7INR_032208chr8+18176955181770391817703918177039118176955,18177039,
MIRLET7GNR_032207chr6+2297151652297152482297152482297152481229715165,229715248,
MIR217NR_032197chr1+6385076396385077216385077216385077211638507639,638507721,

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