Schema for refFlat
  Database: oryLat2    Primary Table: refFlat    Row Count: 903   Data last updated: 2020-08-19
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName b3galt6varchar(255) values Name of gene as it appears in genome browser.
name NM_001104782varchar(255) values Name of gene
chrom chr5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 29835214int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 29836265int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 29835239int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 29836259int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 29835214,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 29836265,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)
      oryLat2.mrnaOrientInfo.name (via refFlat.name)
      oryLat2.refGene.name (via refFlat.name)
      oryLat2.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
b3galt6NM_001104782chr5-29835214298362652983523929836259129835214,29836265,
LOC100049415NM_001104796chr22-18140240181463901814040018146386918140240,18140547,18140887,18141100,18141453,18141769,18142317,18144638,18146368,18140434,18140686,18141020,18141361,18141673,18141857,18142459,18144740,18146390,
cfblNM_001104805chr14+133214691333016313321490133300861813321469,13322384,13322671,13322975,13324198,13324473,13325626,13325873,13326147,13326333,13327052,13327269,13327609,13327835,13 ...13321542,13322588,13322857,13323152,13324285,13324613,13325771,13325999,13326252,13326471,13327162,13327402,13327748,13327912,13 ...
cyp17NM_001105094scaffold521-1784231857051792471856648178423,179932,180153,180450,183683,183872,185143,185352,179531,180036,180323,180672,183770,184108,185282,185705,
foxl1NM_001122919chr6+21541180215429322154158921542570121541180,21542932,
col1a1aNM_001122918chr8-240227842404147524024102240413104924022784,24024415,24024804,24025087,24025456,24025645,24025799,24025999,24026189,24026527,24026679,24026952,24027143,24027398,24 ...24024249,24024658,24024995,24025367,24025564,24025699,24025907,24026053,24026297,24026581,24026787,24027060,24027305,24027452,24 ...
fabp7NM_001122917chr24-390971939106773909731391064443909719,3910049,3910278,3910571,3909782,3910151,3910451,3910677,
pitx2NM_001122916ultracontig115+482887448309604829050483096034828874,4829584,4830402,4829243,4829784,4830960,
lhx3NM_001122915chr12-10183324101932001018332410192865610183324,10185778,10187073,10189022,10189336,10192796,10183758,10185941,10187228,10189227,10189516,10193200,
LOC100144364NM_001122914chr6+22368382223739882236838222373988422368382,22369799,22372249,22373727,22368740,22369886,22372425,22373988,

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