Schema for refFlat
  Database: hg17    Primary Table: refFlat    Row Count: 78,119   Data last updated: 2020-08-21
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName C22orf42varchar(255) values Name of gene as it appears in genome browser.
name NM_001010859varchar(255) values Name of gene
chrom chr22varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 30869546int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 30879844int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 30870080int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 30879756int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 30869546,30870293,30870859,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 30870154,30870321,30871020,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg17.kgAlias.alias (via refFlat.geneName)
      hg17.kgSpAlias.alias (via refFlat.geneName)
      hg17.kgXref.geneSymbol (via refFlat.geneName)
      hgFixed.refLink.name (via refFlat.geneName)
      visiGene.gene.name (via refFlat.geneName)
      hg17.altGraphX.mrnaRefs (via refFlat.name)
      hg17.ccdsInfo.mrnaAcc (via refFlat.name)
      hg17.dupSpMrna.dupMrnaID (via refFlat.name)
      hg17.dupSpMrna.mrnaID (via refFlat.name)
      hg17.kgXref.refseq (via refFlat.name)
      hg17.knownToRefSeq.value (via refFlat.name)
      hg17.mrnaOrientInfo.name (via refFlat.name)
      hg17.mrnaRefseq.mrna (via refFlat.name)
      hg17.mrnaRefseq.refseq (via refFlat.name)
      hg17.refGene.name (via refFlat.name)
      hg17.refSeqAli.qName (via refFlat.name)
      hg17.spMrna.mrnaID (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
C22orf42NM_001010859chr22-30869546308798443087008030879756930869546,30870293,30870859,30871532,30872027,30872607,30873102,30874784,30879524,30870154,30870321,30871020,30871560,30872092,30872635,30873167,30874859,30879844,
GPR75-ASB3NM_001164165chr2-538091045399882153809290539987161053809104,53832671,53839058,53853171,53855353,53867499,53868245,53889570,53904164,53998615,53809478,53832802,53839316,53853369,53855531,53867635,53868358,53889729,53904373,53998821,
PPP6R3NM_001164162chr11+679847956813937768061708681371612467984795,68043544,68061702,68068881,68072110,68075164,68078188,68082609,68088346,68091057,68093791,68095083,68098152,68100001,68 ...67984871,68043695,68061935,68069068,68072248,68075230,68078301,68082723,68088476,68091210,68093941,68095148,68098268,68100087,68 ...
FCGR1CPNR_027484chr1+1461823661461913761461913761461913767146182366,146182842,146183675,146188070,146189746,146190928,146191314,146182447,146182863,146183930,146188325,146190030,146191305,146191376,
RNF167NM_001320363chr17+4784307478926247851374789056104784307,4784962,4785116,4786380,4786616,4786890,4787218,4787465,4788597,4788754,4784400,4785033,4785197,4786506,4786704,4786981,4787324,4787559,4788678,4789262,
NUDCD2NM_001329991chr5-1628061091628196861628135501628186174162806109,162816512,162817145,162818578,162813634,162816664,162817194,162819686,
KLHL36NM_001303451chr16+83239617832587938324197483253240483239617,83241958,83247977,83252684,83239756,83242037,83249020,83258793,
SRRM1NM_001303449chr1+247153552474507824718469247440831824715355,24717780,24718463,24720655,24721767,24723205,24724230,24724709,24726651,24732515,24733106,24734456,24734979,24738611,24 ...24715529,24717870,24718586,24720826,24721883,24723409,24724425,24724829,24726920,24732596,24733193,24734601,24735021,24738722,24 ...
PPME1NM_001271593chr11+735599817364339673560114736422031473559981,73592420,73593045,73611004,73613897,73618937,73619604,73624593,73627825,73634726,73635771,73639646,73640340,73642184,73560215,73592514,73593138,73611062,73613949,73619092,73619695,73624659,73627949,73634898,73635816,73639711,73640408,73643396,
ATP11A-AS1NR_046661chr13-1124477631124570461124570461124570462112447763,112456808,112449755,112457046,

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