Schema for refFlat
  Database: gorGor4    Primary Table: refFlat    Row Count: 474   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName MIR887varchar(255) values Name of gene as it appears in genome browser.
name NR_106417varchar(255) values Name of gene
chrom chr17varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 79644622int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 79644736int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 79644736int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 79644736int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 79644622,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 79644736,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      gorGor4.mrnaOrientInfo.name (via refFlat.name)
      gorGor4.refGene.name (via refFlat.name)
      gorGor4.refSeqAli.qName (via refFlat.name)
      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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
MIR887NR_106417chr17-79644622796447367964473679644736179644622,79644736,
MIR503NR_106416chrX-1346016971346018101346018101346018101134601697,134601810,
LHBNM_001365012chr19-48279645482806574827964548280657348279645,48280122,48280642,48279888,48280290,48280657,
TMEM275NM_001357077chr1-47140242471411664714024247140776247140242,47141151,47140863,47141166,
ERVV-2NM_001308065chr19+52396024523976325239602452397632152396024,52397632,
ERVW-1NM_001304541chr7+85685153856867708568515385686770185685153,85686770,
AZIN2NM_001293723chr1+333241463336432233325232333639731133324146,33324373,33325160,33326928,33335743,33336975,33338225,33340379,33341740,33361691,33363834,33324277,33324491,33325337,33327102,33335916,33337110,33338391,33340542,33341853,33361906,33364322,
MIR487BNR_106318chr14+85069465850695758506957585069575185069465,85069575,
MIR181DNR_106313chr19+13652085136521931365219313652193113652085,13652193,
MIR106BNR_106278chr7+77984053779841357798413577984135177984053,77984135,

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