Schema for xenoRefFlat
  Database: hg17    Primary Table: xenoRefFlat    Row Count: 205,346   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 LOC542758varchar(255) values Name of gene as it appears in genome browser.
name NM_001112267varchar(255) values Name of gene
chrom chr22varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 35951852int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 35962197int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 35951852int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 35962197int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 35951852,35952480,35953349,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 35951930,35952534,35953457,...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hg17.altGraphX.mrnaRefs (via xenoRefFlat.name)
      hg17.xenoMrna.qName (via xenoRefFlat.name)
      hg17.xenoRefGene.name (via xenoRefFlat.name)
      hg17.xenoRefSeqAli.qName (via xenoRefFlat.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
LOC542758NM_001112267chr22-35951852359621973595185235962197435951852,35952480,35953349,35962125,35951930,35952534,35953457,35962197,
LOC542748NM_001112257chr11-73363750733956697336375073395669573363750,73364269,73365349,73394420,73395609,73363813,73364332,73365439,73394462,73395669,
ZxdbNM_001081473chrX+575013925750655357501502575039141357501392,57501722,57501774,57502000,57502111,57502158,57502288,57503500,57503631,57505830,57505922,57506258,57506481,57501721,57501740,57501903,57502111,57502141,57502251,57503461,57503622,57503924,57505860,57505955,57506390,57506553,
S100A11NM_001004045chr7+1024964151024967451024964151024967062102496415,102496697,102496685,102496745,
PCSK2NM_001004044chr20+171559251741091917155950174107151317155925,17188884,17286971,17289176,17297884,17337907,17358079,17365354,17382386,17384992,17393970,17410229,17410841,17156127,17188989,17287085,17289285,17297922,17337984,17358170,17365528,17382602,17385093,17394199,17410778,17410919,
Olr531NM_001001051chr11-55437722554925305543772255492530255437722,55491768,55437860,55492530,
ND-20LNM_001300655chr19+134187213464871341872134648741341872,1342117,1344238,1346389,1342049,1342142,1344329,1346487,
Tor1aip2NM_022329chr1-1765654161765662661765655721765659683176565416,176565562,176566108,176565476,176566031,176566266,
RalbNM_022327chr2+1207266721207670891207524701207670665120726672,120752460,120759679,120763385,120766949,120726747,120752584,120759888,120763566,120767089,
CtsmNM_022326chr10-52135761521379215213576152137921552135761,52136664,52137118,52137199,52137804,52135836,52136679,52137169,52137340,52137921,

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