Schema for refFlat
  Database: panPan1    Primary Table: refFlat    Row Count: 117   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 MIR107varchar(255) values Name of gene as it appears in genome browser.
name NR_106561varchar(255) values Name of gene
chrom JH650556varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 519856int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 519937int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 519937int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 519937int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 519856,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 519937,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)
      panPan1.mrnaOrientInfo.name (via refFlat.name)
      panPan1.refGene.name (via refFlat.name)
      panPan1.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIR107NR_106561JH650556-5198565199375199375199371519856,519937,
TLR5NM_001279191JH650419-5907295933065907295933061590729,593306,
MYD88NM_001279189JH650558-487923848818244879238488182454879238,4879676,4879956,4880526,4881496,4879393,4879768,4880137,4880661,4881824,
MIR29B-1NR_106557JH650376+11122419111225001112250011122500111122419,11122500,
MIR99ANR_106554JH650491+252212125222022522202252220212522121,2522202,
MIR187NR_106573JH650601+11059122110592311105923111059231111059122,11059231,
MIR19B-2NR_106609JH650406-340126334013593401359340135913401263,3401359,
MIR19B-1NR_106598JH650624+10418958104190451041904510419045110418958,10419045,
MIR106ANR_106608JH650406-340179034018713401871340187113401790,3401871,
MIR19ANR_106596JH650624+10418657104187391041873910418739110418657,10418739,

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