Schema for xenoRefFlat
  Database: aplCal1    Primary Table: xenoRefFlat    Row Count: 246,163   Data last updated: 2020-08-18
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName ZBTB17varchar(255) values Name of gene as it appears in genome browser.
name NM_001324137varchar(255) values Name of gene
chrom scaffold_2398varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 7933int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 8191int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 7933int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 8191int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 7933,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 8191,longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        aplCal1.xenoRefGene.name (via xenoRefFlat.name)
      aplCal1.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
ZBTB17NM_001324137scaffold_2398+793381917933819117933,8191,
ZBTB17NM_001324137scaffold_2398+10095102151009510215110095,10215,
ZBTB17NM_001324137scaffold_7405-300134433001344343001,3135,3230,3422,3030,3157,3281,3443,
ZBTB17NM_001324137scaffold_9-1636225163721636225163722163622,516342,163678,516372,
PRKAA1NM_001109802scaffold_57-20064322278520064321597211200643,202295,202850,202904,209664,212344,213805,214363,215913,217794,222722,200697,202349,202853,202976,209709,212416,213889,214511,216004,217930,222785,
NRKNM_001031126scaffold_851-38226383763822638376138226,38376,
Ahcyl2NM_021414scaffold_8465+779485177948512779,4747,870,4851,
Ahcyl2NM_021414scaffold_876+104912778104912778141049,1349,3997,4193,5400,5482,6787,7365,8100,8297,9152,9803,10600,12656,1171,1352,4175,4198,5440,5486,6847,7456,8265,8300,9248,9872,10679,12778,
galnt11NM_001006903scaffold_319-2199682258992199682258994219968,220937,221618,225806,220058,221091,221737,225899,
myo6aNM_001004111scaffold_517-1774072656692656672656695177407,208344,255943,258490,265642,177440,208360,255956,258521,265669,

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