Schema for refFlat
  Database: panPan2    Primary Table: refFlat    Row Count: 218   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 AZIN2varchar(255) values Name of gene as it appears in genome browser.
name NM_001293718varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 33550139int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 33589402int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 33551275int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 33589052int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 33550139,33550413,33550626,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 33550320,33550534,33550838,...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)
      panPan2.mrnaOrientInfo.name (via refFlat.name)
      panPan2.refGene.name (via refFlat.name)
      panPan2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
AZIN2NM_001293718chr1+335501393358940233551275335890521233550139,33550413,33550626,33551203,33552970,33561068,33562300,33563556,33565713,33567073,33586771,33588913,33550320,33550534,33550838,33551380,33553144,33561241,33562435,33563722,33565876,33567186,33586986,33589402,
MIR101NR_106556chr1-66194649661947246619472466194724166194649,66194724,
MIR26ANR_106545chr3+38151349381514263815142638151426138151349,38151426,
MIR197NR_106586chr1+1112041261112042011112042011112042011111204126,111204201,
OAZ3NM_001290340chr1+1307650021307739741307652891307738595130765002,130769316,130770210,130772811,130773716,130765321,130769453,130770386,130772897,130773974,
OAZ3NM_001301415chr1+1307688081307739741307688751307738595130768808,130769316,130770210,130772811,130773716,130769042,130769453,130770386,130772897,130773974,
SLAMF9NM_001302655chr1-1392241381392266141392241381392266144139224138,139224739,139225779,139226568,139224344,139225008,139226125,139226614,
MIR214NR_106578chr1-1513465541513466641513466641513466641151346554,151346664,
MIR205NR_106577chr1+1898126561898127661898127661898127661189812656,189812766,
MIR1NR_106589chr18-18704312187043971870439718704397118704312,18704397,

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