Schema for refFlat
  Database: equCab3    Primary Table: refFlat    Row Count: 1,948   Data last updated: 2019-07-17
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName RPL7varchar(255) values Name of gene as it appears in genome browser.
name NM_001163864varchar(255) values Name of gene
chrom chr9varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 13566995int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 13570155int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 13567001int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 13569776int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 13566995,13567801,13568202,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 13567015,13567913,13568369,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      equCab3.mrnaOrientInfo.name (via refFlat.name)
      equCab3.refGene.name (via refFlat.name)
      equCab3.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
RPL7NM_001163864chr9+13566995135701551356700113569776713566995,13567801,13568202,13568891,13569147,13569567,13570091,13567015,13567913,13568369,13569029,13569257,13569777,13570155,
CD1B1NM_001163862chr5-35596724356003013559701735600278635596724,35597747,35598227,35598712,35599666,35600217,35597039,35597841,35598506,35598991,35599933,35600301,
GFAPNM_001163861chr11+18815118188226921881513218822692918815118,18816467,18816722,18817558,18818910,18819302,18820100,18821906,18822650,18815578,18816528,18816818,18817720,18819036,18819523,18820144,18821992,18822692,
NR0B1NM_001163859chrX-24727816247325482472781624732548224727816,24731377,24728061,24732548,
CHIT1NM_001143797chr30-313073563131987031307538313197891131307356,31308326,31309778,31310205,31312806,31313662,31313985,31315396,31316044,31318450,31319764,31307783,31308453,31309892,31310391,31312930,31313787,31314151,31315453,31316246,31318480,31319870,
SMC3NM_001308957chr1-209105622094397620911015209438972920910562,20911989,20912751,20913080,20913622,20913920,20914710,20915307,20916031,20917519,20919089,20921140,20922853,20923347,20 ...20911087,20912096,20912929,20913272,20913835,20914168,20914819,20915415,20916190,20917671,20919242,20921291,20922995,20923508,20 ...
HELZNM_001301207chr11-140245951418851014024864141615073114024595,14028946,14051186,14052788,14053434,14057956,14063715,14065644,14066598,14076475,14082987,14084989,14099123,14100555,14 ...14025199,14029199,14051703,14053029,14054005,14058036,14063923,14065835,14066650,14076680,14083216,14085173,14099271,14100701,14 ...
ARF2NM_001242541chr11-17948586179643881794884917964380417948586,17950930,17958077,17964232,17949011,17951055,17958188,17964388,
RXFP2NM_001163868chr17+110600941111739911060207111172991811060094,11076304,11078897,11081803,11082737,11091272,11091957,11093650,11094942,11097871,11099357,11102797,11102976,11105207,11 ...11060256,11076451,11078975,11081909,11082809,11091344,11092029,11093722,11095014,11097943,11099429,11102869,11103048,11105279,11 ...
CYP11A1NM_001082521chr1+1204822031204945341204822031204945349120482203,120485827,120487631,120488828,120489791,120492738,120493192,120493745,120494402,120482472,120485983,120487831,120489032,120489949,120492905,120493271,120493943,120494534,

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