Schema for refFlat
  Database: calJac3    Primary Table: refFlat    Row Count: 235   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CYP2E1varchar(255) values Name of gene as it appears in genome browser.
name NM_001267751varchar(255) values Name of gene
chrom chr12varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 121685485int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 121694607int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 121685521int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 121694578int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 121685485,121686548,1216893...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 121685698,121686708,1216895...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      calJac3.mrnaOrientInfo.name (via refFlat.name)
      calJac3.refGene.name (via refFlat.name)
      calJac3.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
CYP2E1NM_001267751chr12+1216854851216946071216855211216945788121685485,121686548,121689398,121689920,121690437,121692866,121693425,121694387,121685698,121686708,121689548,121690081,121690615,121692938,121693567,121694607,
ALPLNM_001185034chr7+554891085556172455538058555609751255489108,55537959,55544454,55544916,55546599,55547501,55551806,55553874,55556797,55559191,55559904,55560709,55489198,55538119,55544574,55545032,55546774,55547677,55551950,55553944,55556932,55559383,55560024,55561724,
GH1NM_001290346chr5-82659914826614908266001682661428582659914,82660428,82660685,82661013,82661418,82660214,82660593,82660805,82661174,82661490,
IL2RGNM_001301846chrX-62991168629957286299138562995714862991168,62991951,62992272,62993107,62994008,62994673,62995058,62995602,62991571,62992021,62992369,62993270,62994148,62994858,62995212,62995728,
APOBEC3ANM_001301845chr1+2013056462013104832013056462013104833201305646,201307371,201310194,201305675,201307528,201310483,
LHCGRNM_001301843chr14+59027419590705165902741959070470959027419,59029488,59032857,59034856,59035019,59045009,59050172,59054307,59069317,59027491,59029563,59032932,59034931,59035097,59045078,59050247,59054493,59070516,
OAZ2NM_001301337chr10-701812470332497019249703304557018124,7019625,7020542,7021578,7033025,7019380,7019711,7020718,7021733,7033249,
AZIN2NM_001293699chr7+673225376736007667323601673598571067322537,67322742,67323549,67325368,67334433,67335578,67337468,67340627,67341980,67359717,67322649,67322863,67323706,67325542,67334606,67335713,67337634,67340790,67342093,67360076,
AZIN1NM_001291457chr16+916626199170100291683873916987371291662619,91668393,91683778,91687038,91688089,91691548,91693093,91693574,91694749,91697445,91697884,91698625,91662998,91668532,91683975,91687212,91688262,91691683,91693175,91693649,91694912,91697561,91698099,91701002,
AZIN1NM_001291456chr16+916626199170100291683873916987371391662619,91668393,91677308,91683778,91687038,91688089,91691548,91693093,91693574,91694749,91697445,91697884,91698625,91662998,91668532,91677454,91683975,91687212,91688262,91691683,91693175,91693649,91694912,91697561,91698099,91701002,

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