Schema for refFlat
  Database: strPur1    Primary Table: refFlat    Row Count: 934   Data last updated: 2020-09-02
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName LOC373206varchar(255) values Name of gene as it appears in genome browser.
name NM_214477varchar(255) values Name of gene
chrom Scaffold1582varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 46866int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 79743int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 46866int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 79444int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 46866,79283,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 46999,79743,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)
      strPur1.mrnaOrientInfo.name (via refFlat.name)
      strPur1.refGene.name (via refFlat.name)
      strPur1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LOC373206NM_214477Scaffold1582-46866797434686679444246866,79283,46999,79743,
LOC373206NM_214477Scaffold1841-88926673889266738889,2656,8578,9635,10951,13588,14969,26545,999,2745,8665,9684,11010,13728,15049,26673,
LOC575855NM_001242653Scaffold53336-604680046046800436046,6771,7848,6322,6921,8004,
H2ANM_001014426Scaffold88164+1585331585331158,533,
snailNM_214660Scaffold79000-163648062182464831636,2771,4563,2759,3135,4806,
LOC373183NM_001123498Scaffold52351-156153061926530641561,3167,4408,5175,2127,3221,4552,5306,
PDE1NM_001098448Scaffold410+329957785832995778581132995,34270,39768,40592,56856,63042,66237,73376,76509,77194,77774,33071,34547,39954,40659,56969,63183,66338,73502,76611,77315,77858,
Mir2013NR_036418Scaffold28231-461847194719471914618,4719,
Mir2012NR_036417Scaffold104536-35317354013540135401135317,35401,
Mir219NR_036415Scaffold25727-923393349334933419233,9334,

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