Schema for refFlat
  Database: ponAbe3    Primary Table: refFlat    Row Count: 3,434   Data last updated: 2018-10-26
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName SH3BP5Lvarchar(255) values Name of gene as it appears in genome browser.
name NM_001132368varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 97657int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 112869int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 98472int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 111413int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 97657,98041,106467,106689,1...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 97698,98655,106530,106818,1...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)
      ponAbe3.mrnaOrientInfo.name (via refFlat.name)
      ponAbe3.refGene.name (via refFlat.name)
      ponAbe3.refSeqAli.qName (via refFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
SH3BP5LNM_001132368chr1+9765711286998472111413797657,98041,106467,106689,108748,110183,110942,97698,98655,106530,106818,108910,110357,112869,
SCCPDHNM_001133324chr1-2285969233498322865092334947122285969,2287671,2289178,2297160,2297311,2298245,2298971,2315743,2319605,2323884,2332059,2334757,2286615,2287753,2289290,2297217,2297431,2298363,2299102,2315793,2319735,2323965,2332172,2334983,
EFCAB2NM_001131911chr1-401402241747124017942417468374014022,4063344,4063547,4064840,4088536,4124529,4174658,4018181,4063411,4063590,4064920,4088609,4124614,4174712,
DESI2NM_001133555chr1-444009645009774443306450096854440096,4461856,4464547,4467170,4500926,4443540,4461998,4464641,4467243,4500977,
KMONM_001132677chr1-7537030759473175584297594669157537030,7538823,7538972,7540257,7542351,7558420,7560454,7562022,7564709,7566289,7571401,7576080,7577340,7578122,7594615,7537365,7538882,7539074,7540340,7542409,7558568,7560576,7562094,7564875,7566377,7571450,7576170,7577438,7578192,7594731,
FHNM_001132068chr1+7607337762948176073697629257107607337,7609832,7613428,7615090,7618359,7620968,7622877,7624552,7626521,7629114,7607501,7609967,7613539,7615267,7618542,7621134,7623081,7624680,7626675,7629481,
CHRM3NM_001132433chr1-923729297579519238415924018869237292,9320938,9471485,9517977,9598334,9757686,9240207,9321065,9471588,9518030,9598443,9757951,
MTRNM_001132713chr1-124235301248794112425651124757982112423530,12426167,12427737,12428712,12434261,12436255,12439192,12440340,12444725,12450773,12451795,12462744,12463955,12465024,12 ...12425738,12426280,12427930,12428913,12434458,12436411,12439268,12440439,12444807,12450894,12451863,12462845,12464063,12465177,12 ...
CA11NM_001135496chr19-47015135470231804701523247022731947015135,47015995,47016412,47016657,47016896,47017203,47021525,47022501,47022664,47015258,47016161,47016567,47016730,47016992,47017389,47021668,47022576,47023180,
TBCENM_001132054chr1-139236251401424213923842139981331713923625,13924154,13929618,13930625,13933893,13935353,13936199,13936357,13936966,13938869,13942364,13945924,13953219,13958177,13 ...13923935,13924246,13929678,13930694,13934047,13935506,13936264,13936422,13937062,13938946,13942464,13946024,13953308,13958363,13 ...

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