Schema for refFlat
  Database: panTro5    Primary Table: refFlat    Row Count: 2,968   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 PATR-Fvarchar(255) values Name of gene as it appears in genome browser.
name NM_001129198varchar(255) values Name of gene
chrom chr6varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 29948683int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 29951682int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 29948687int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 29951631int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 29948683,29948881,29949396,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 29948751,29949151,29949672,...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)
      panTro5.mrnaOrientInfo.name (via refFlat.name)
      panTro5.refGene.name (via refFlat.name)
      panTro5.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
PATR-FNM_001129198chr6+29948683299516822994868729951631729948683,29948881,29949396,29950254,29950670,29951234,29951626,29948751,29949151,29949672,29950530,29950787,29951267,29951682,
ARPC5NM_001246501chr1-1622511981622607311622525301622606244162251198,162255443,162258046,162260481,162252593,162255620,162258119,162260731,
UBAC2NM_001246491chr13+84897459850800038489751485078910984897459,84934945,84939021,84939702,85007512,85011456,85033760,85061219,85078802,84897545,84935073,84939141,84939812,85007636,85011504,85034006,85061339,85080003,
DCTN5NM_001246500chr16+23070097230988292307017123096110723070097,23071580,23087481,23090155,23094591,23096012,23098031,23070219,23071649,23087600,23090267,23094694,23096539,23098829,
MED20NM_001246490chr6-42368200423836074236991742383538442368200,42372128,42379626,42383524,42370133,42372382,42379781,42383607,
ACP2NM_001246489chr11-474893184749843147489727474984061147489318,47492335,47492630,47492851,47494347,47494917,47495086,47495294,47497259,47497656,47498292,47489861,47492511,47492737,47492934,47494480,47495007,47495185,47495447,47497346,47497752,47498431,
RPL7ANM_001246603chr9+1116407621116439691116407871116439098111640762,111641465,111642097,111642458,111642786,111643143,111643550,111643804,111640790,111641586,111642247,111642599,111642866,111643274,111643620,111643969,
CAP1NM_001246593chr1+394482673947969739467434394796321339448267,39467421,39468154,39469822,39472341,39472588,39474318,39475636,39477787,39478256,39478528,39478934,39479548,39448495,39467546,39468258,39469900,39472485,39472674,39474424,39475814,39477972,39478380,39478611,39479078,39479697,
MAGEB4NM_001246602chrX+30427734304300143042795830428999130427734,30430014,
CALUNM_001246592chr7+1332579751332901051332672381332878037133257975,133267227,133272906,133277510,133278419,133286098,133287698,133258058,133267459,133273100,133277677,133278480,133286298,133290105,

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