Schema for refFlat
  Database: panTro2    Primary Table: refFlat    Row Count: 2,852   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 RLN2varchar(255) values Name of gene as it appears in genome browser.
name NM_001122774varchar(255) values Name of gene
chrom chr9_randomvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 4699650int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 4699861int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4699650int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 4699861int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 4699650,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4699861,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)
      panTro2.mrnaOrientInfo.name (via refFlat.name)
      panTro2.refGene.name (via refFlat.name)
      panTro2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
RLN2NM_001122774chr9_random-469965046998614699650469986114699650,4699861,
RLN2NM_001122774chrUn-52725442527256535272544252725653152725442,52725653,
TRIM15NM_001045508chr6+30807811308164303080781130816430730807811,30811297,30812422,30813363,30814580,30815055,30815912,30808192,30811393,30812653,30813386,30814696,30815088,30816430,
TFDP1NM_001251920chrX-37278011372801453727891537280145237278011,37279813,37279813,37280145,
COX4I1NM_001251915chr16+86097607861048978609912286104793586097607,86099121,86102854,86103651,86104656,86097669,86099195,86103022,86103783,86104897,
TMEM97NM_001251914chr17-29023946290343902902584629034251329023946,29026989,29034125,29026103,29027134,29034390,
VPS25NM_001252014chr17-14747720147539511474825214753917614747720,14751058,14751919,14752688,14753514,14753864,14748365,14751134,14752008,14752742,14753660,14753951,
ARPC3NM_001251913chr12-1117123721117278881117123721117278257111712372,111713334,111713781,111714320,111717254,111722595,111727819,111712435,111713429,111713908,111714389,111717331,111722695,111727888,
ABITRAMNM_001251912chr9+1083495911083561261083496851083548556108349591,108350833,108351493,108354365,108354554,108354717,108349764,108350885,108351623,108354442,108354624,108356126,
FUNDC2NM_001251911chr5-42425978424267204242615042426720142425978,42426720,

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