Schema for refFlat
  Database: felCat5    Primary Table: refFlat    Row Count: 449   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 LOC493739varchar(255) values Name of gene as it appears in genome browser.
name NM_001009233varchar(255) values Name of gene
chrom chrD4varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 75158302int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 75162634int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 75158561int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 75162617int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 75158302,75159500,75159747,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 75158571,75159546,75159843,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      felCat5.mrnaOrientInfo.name (via refFlat.name)
      felCat5.refGene.name (via refFlat.name)
      felCat5.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
LOC493739NM_001009233chrD4-75158302751626347515856175162617775158302,75159500,75159747,75160167,75160997,75162033,75162527,75158571,75159546,75159843,75160278,75161068,75162170,75162634,
CCR5NM_001009248chrA2+15588781155898401558878115589840115588781,15589840,
ADRB2NM_001009247chrA1-1977587961977600531977587961977600531197758796,197760053,
NPPBNM_001009244chrC1-787747878789547877656787886537877478,7878247,7878739,7877673,7878503,7878954,
RHONM_001009242chrA2+53225668532314125322566853231412553225668,53228483,53229925,53230197,53231301,53226029,53228652,53230091,53230437,53231412,
TNNI3NM_001009237chrE2+314149831447493141550314467993141498,3141825,3141980,3142473,3142791,3143313,3143953,3143987,3144595,3141561,3141835,3142067,3142515,3142923,3143403,3143987,3144129,3144749,
CTLA4NM_001009236chrC1+1895139841895201851895140521895190954189513984,189516796,189517584,189518990,189514161,189517144,189517694,189520185,
CASP3NM_001009338chrB1-13936659139586331393687513945539713936659,13938494,13939385,13939880,13943024,13945486,13958573,13937105,13938615,13939561,13940009,13943149,13945551,13958633,
GH1NM_001009337chrE1-47922078479237324792214347923691547922078,47922619,47922940,47923272,47923681,47922344,47922781,47923057,47923433,47923732,
FELCATV1R1NM_001167473chrE2-11944512119454211194451211945421111944512,11945421,

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