Schema for refFlat
  Database: bosTau2    Primary Table: refFlat    Row Count: 17,810   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 IPO5varchar(255) values Name of gene as it appears in genome browser.
name NM_001372122varchar(255) values Name of gene
chrom chr12varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 39364882int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 39423930int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 39366142int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 39399405int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 28int(10) unsigned range Number of exons
exonStarts 39364882,39366825,39368188,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 39366229,39366967,39368417,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.refLink.name (via refFlat.geneName)
      bosTau2.refGene.name (via refFlat.name)
      bosTau2.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)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
IPO5NM_001372122chr12-393648823942393039366142393994052839364882,39366825,39368188,39368999,39370070,39371232,39371376,39372406,39373750,39375860,39376079,39377476,39378975,39380946,39 ...39366229,39366967,39368417,39369219,39370193,39371288,39371488,39372579,39373847,39375982,39376212,39377560,39379194,39381120,39 ...
AQP1NM_174702chr4-36121489361356883612332836135672436121489,36123966,36124344,36135282,36123508,36124047,36124509,36135688,
FAM13ANM_174692chr6+16005482160204091600569616020409216005482,16020367,16005725,16020409,
FAM13ANM_174692chr6+192567001932156719256700193187511619256700,19259423,19265644,19277692,19278128,19287550,19296196,19296871,19297741,19298641,19299512,19308439,19309820,19315460,19 ...19256756,19259600,19265831,19277769,19278171,19287698,19296410,19297010,19297823,19298862,19299596,19308535,19309904,19315657,19 ...
HSD17B14NM_174701chr18-48021636480419194802180948041876948021636,48022073,48022270,48022712,48035835,48040240,48040835,48041107,48041788,48021983,48022170,48022338,48022817,48035927,48040307,48040918,48041146,48041919,
FDXRNM_174691chr19+51817477518197915181747751819417951817477,51817696,51817869,51817890,51817979,51817993,51818030,51818982,51819286,51817565,51817857,51817890,51817896,51817993,51818029,51818151,51819153,51819791,
FDXRNM_174691scaffold4750-2637032263698211263,673,927,950,1043,1248,1269,1275,1281,6024,6903,365,787,940,1043,1050,1268,1274,1281,1344,6122,7032,
KIAA1549NM_001080267chr4+599790256010488259979914600993782059979025,60023918,60027863,60029011,60031211,60033557,60036603,60037841,60046766,60049945,60058678,60060621,60065098,60068346,60 ...59980049,60026614,60027952,60029189,60031342,60033741,60036663,60037990,60046944,60050130,60058875,60060737,60065301,60068570,60 ...
GRIA2NM_001076321scaffold593-54373198150543731979321254373,59023,59883,61879,62680,63052,82664,87659,92824,107073,197154,197844,54572,59394,60090,61990,62785,63220,82826,87713,93021,107313,197295,198150,
GRIA2NM_001076321scaffold3296-66575740767090474076466575,70901,72308,73827,70507,71150,72423,74076,

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