Schema for refFlat
  Database: canFam1    Primary Table: refFlat    Row Count: 2,060   Data last updated: 2020-08-20
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CUBNvarchar(255) values Name of gene as it appears in genome browser.
name NM_001003148varchar(255) values Name of gene
chrom chr2varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 20363718int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 20621509int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 20363791int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 20621169int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 68int(10) unsigned range Number of exons
exonStarts 20363718,20364294,20365329,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 20363904,20364424,20365425,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      canFam1.refGene.name (via refFlat.name)
      canFam1.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
CUBNNM_001003148chr2+203637182062150920363791206211696820363718,20364294,20365329,20365948,20368791,20369560,20374735,20375813,20378241,20379271,20381252,20381564,20382914,20385832,20 ...20363904,20364424,20365425,20365987,20368893,20369664,20374862,20375976,20378373,20379367,20381371,20381751,20383027,20386067,20 ...
PDE6DNM_001003156chr25-46635426466888244663594046688765546635426,46637932,46638709,46639468,46688715,46636022,46638038,46638835,46639557,46688824,
PTH1RNM_001003155chr20-447604464477991744760557447796561444760446,44761469,44761631,44762190,44762524,44762914,44764551,44765197,44765530,44765751,44765969,44767680,44769638,44779581,44760953,44761511,44761773,44762285,44762591,44762975,44764705,44765390,44765625,44765870,44766080,44767815,44769741,44779917,
TRDNNM_001003154chr1-654142116577400265414225657737983965414211,65417838,65420034,65439584,65442387,65443432,65443840,65444610,65446386,65447570,65449767,65450995,65453118,65455141,65 ...65414365,65417877,65420076,65439608,65442432,65443468,65443879,65444637,65446407,65447615,65449785,65451052,65453166,65455171,65 ...
RAB1ANM_001003153chr10-67944725679705986794479967970587667944725,67945244,67946949,67951221,67955976,67970564,67944997,67945376,67947045,67951317,67956049,67970598,
RAB1ANM_001003153chr31+371152137118033711655371180313711521,3711803,
RAB8ANM_001003152chr20-49196141492134484919626849213439849196141,49199579,49200981,49201642,49203219,49206849,49208766,49213315,49196361,49199630,49201047,49201732,49203297,49206910,49208827,49213448,
CXCR2NM_001003151chr37+27818880278243082782293727824014227818880,27822912,27818944,27824308,
MT4NM_001003150chr2-60278663602812506027885560281211360278663,60279495,60281180,60278947,60279561,60281250,
MT2ANM_001003149chr2-60245906602468066024608160246753360245906,60246371,60246725,60246173,60246437,60246806,

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