Schema for refFlat
  Database: rheMac8    Primary Table: refFlat    Row Count: 6,507   Data last updated: 2020-08-22
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName CDKN1Bvarchar(255) values Name of gene as it appears in genome browser.
name NM_001261005varchar(255) values Name of gene
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 13371435int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 13375419int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 13371913int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 13373044int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 13371435,13372922,13375129,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 13372388,13373052,13375419,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)
      rheMac8.mrnaOrientInfo.name (via refFlat.name)
      rheMac8.refGene.name (via refFlat.name)
      rheMac8.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
CDKN1BNM_001261005chr11+13371435133754191337191313373044313371435,13372922,13375129,13372388,13373052,13375419,
SERPINI1NM_001260895chr2-1261791531262658651261793361262141259126179153,126180126,126181620,126197355,126208540,126210513,126212653,126213875,126265751,126179413,126180216,126181707,126197453,126208745,126210708,126212884,126214143,126265865,
LARGE1NM_001260905chr10-751609527579466575162218756379331575160952,75164807,75171326,75191269,75203339,75223963,75264520,75267132,75303644,75439122,75478931,75500927,75525485,75637827,75 ...75162416,75165003,75171473,75191548,75203503,75224119,75264646,75267245,75303749,75439294,75479055,75501010,75525787,75638015,75 ...
ING5NM_001194001chr12+1245575071245800771245575251245797508124557507,124560097,124565020,124567036,124567630,124577658,124577929,124579707,124557562,124560169,124565187,124567148,124567724,124577794,124577991,124580077,
NPWNM_001204349chr20+200911920098372009119200983722009119,2009750,2009530,2009837,
DDIT4LNM_001194403chr5-98944699989477339894498098947208398944699,98947117,98947540,98945471,98947257,98947733,
SPINDOCNM_001194689chr14-10745666107602751074574210759972610745666,10754680,10755028,10755310,10755541,10759845,10745954,10754881,10755154,10755460,10755871,10760275,
DDIT3NM_001194700chr11-56308922563106525630922356309821356308922,56309683,56310625,56309595,56309839,56310652,
RPRMLNM_001194690chr16+51681788516827535168202451682387151681788,51682753,
MYRFNM_001194718chr14-125023461253623612504699125362072612502346,12504966,12506435,12506888,12507194,12508937,12509432,12509717,12510474,12510834,12511208,12511355,12512263,12512885,12 ...12504780,12505041,12506541,12506963,12507282,12509189,12509624,12509806,12510543,12510923,12511281,12511516,12512373,12512997,12 ...

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