Schema for refFlat
  Database: felCat3    Primary Table: refFlat    Row Count: 743   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 F9varchar(255) values Name of gene as it appears in genome browser.
name NM_001009377varchar(255) values Name of gene
chrom scaffold_204919varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 74661int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 108120int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 74661int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 108120int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 74661,80893,81258,85896,927...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 74749,81057,81283,86010,928...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      felCat3.mrnaOrientInfo.name (via refFlat.name)
      felCat3.refGene.name (via refFlat.name)
      felCat3.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
F9NM_001009377scaffold_204919+7466110812074661108120774661,80893,81258,85896,92735,106798,107572,74749,81057,81283,86010,92864,106916,108120,
ADRB1NM_001009375scaffold_133254+2122662126512122662126511212266,212651,
MCL1NM_001009374scaffold_127430-356048374719483713560,4837,
MCL1NM_001009374scaffold_48598-011690116920,539,185,1169,
PSIP1NM_001009372scaffold_199457-835719835719483,109,3646,5490,109,129,3765,5719,
PSIP1NM_001009372scaffold_199461-57440920505744092050657440,57449,58285,82136,91972,92005,57449,57465,58400,82276,92004,92050,
CYP17A1NM_001009371scaffold_132920-4176864243874176864243877417686,418482,419410,420888,421758,422198,424102,417969,418586,419586,420976,421988,422337,424387,
PPIANM_001009370scaffold_23723+211522211318421,131,435,1185,52,220,608,1522,
KLRAP1NM_001009834scaffold_83731+920109092010902920,1082,1082,1090,
KITNM_001009837scaffold_215273+16815622076716815622076713168156,175913,176179,177293,212878,214534,215933,216137,216546,216740,218073,220057,220639,168429,176179,176194,177413,212993,214728,216040,216264,216651,216851,218224,220149,220767,

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