Schema for refFlat
  Database: strPur2    Primary Table: refFlat    Row Count: 685   Data last updated: 2020-09-01
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName tpcn3varchar(255) values Name of gene as it appears in genome browser.
name NM_001144977varchar(255) values Name of gene
chrom Scaffold78430varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 9066int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 31265int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 9066int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 31219int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 19int(10) unsigned range Number of exons
exonStarts 9066,10953,12077,18454,1938...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 9351,11036,12198,18580,1950...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)
      strPur2.mrnaOrientInfo.name (via refFlat.name)
      strPur2.refGene.name (via refFlat.name)
      strPur2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
tpcn3NM_001144977Scaffold78430+906631265906631219199066,10953,12077,18454,19382,20143,20990,21621,22167,23204,24230,24862,25433,26107,27261,28040,28609,30268,31070,9351,11036,12198,18580,19505,20262,21095,21748,22369,23349,24395,24927,25512,26177,27493,28131,28723,30390,31265,
COLP4alphaNM_214511Scaffold64639+440360954403609524403,5986,4539,6095,
LOC373365NM_214566Scaffold61317+807542154824841429238075,11577,12506,15912,17508,19956,22548,23220,24793,25647,26583,27245,31437,32057,33454,34431,35641,36126,37299,37821,38754,393 ...8345,11666,12602,15997,17640,20053,22645,23307,24877,25728,26679,27335,31622,32142,33600,34504,35723,36254,37392,37954,38865,395 ...
cyp51NM_001001906Scaffold51709-4205344205341420,534,
ARSNM_214512Scaffold43350+11935200731194919486911935,12049,12080,14774,15912,16710,17488,18806,19995,12049,12079,12322,14924,16025,16933,17653,19975,20073,
GATAcNM_214539Scaffold40010+2575992766952576402766044257599,263975,265405,276226,258289,264121,265528,276695,
LOC373288NM_214523Scaffold48975-465389037546571900521346538,47183,48929,55843,56686,60019,65161,66800,73359,78822,80110,83938,89844,46676,47242,48987,55915,56761,60121,65303,66865,73401,78906,80163,83974,90375,
TCKNM_214522Scaffold72708+1588301661871589231658214158830,160497,161351,162463,158963,160549,161426,166187,
SFK1NM_214618Scaffold80389-473889107328891054738,6136,7115,7319,8774,5663,6918,7284,7529,8910,
SFK1NM_214618Scaffold90851+3634593634591363,459,

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