Schema for xenoRefFlat
  Database: rn3    Primary Table: xenoRefFlat    Row Count: 428,843   Data last updated: 2020-08-23
Format description: A gene prediction with additional geneName field.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
geneName Mtg1varchar(255) values Name of gene as it appears in genome browser.
name NM_199301varchar(255) values Name of gene
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 200087914int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 200100876int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 200088015int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 200100368int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 200087914,200088659,2000903...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 200088124,200088724,2000904...longblob   Exon end positions (or start positions for minus strand item)

Connected Tables and Joining Fields
        hgFixed.gbCdnaInfo.acc (via xenoRefFlat.name)
      hgFixed.gbSeq.acc (via xenoRefFlat.name)
      hgFixed.imageClone.acc (via xenoRefFlat.name)
      rn3.xenoMrna.qName (via xenoRefFlat.name)
      rn3.xenoRefGene.name (via xenoRefFlat.name)
      rn3.xenoRefSeqAli.qName (via xenoRefFlat.name)

Sample Rows
 
geneNamenamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEnds
Mtg1NM_199301chr1+20008791420010087620008801520010036812200087914,200088659,200090348,200094386,200094857,200095173,200096550,200096971,200097409,200099828,200100249,200100738,200088124,200088724,200090453,200094467,200094914,200095264,200096612,200097068,200097491,200099941,200100729,200100876,
Vmn2r89NR_104384chr1+550316919169191691935503,8986,15965,5590,9795,16919,
Gm44NM_001101450chrX-79256869795197967925686979519796379256869,79256915,79519739,79256893,79257490,79519796,
efna3.LNM_001087027chr2-1814487161814496681814487161814496685181448716,181448945,181448968,181449135,181449381,181448782,181448947,181449032,181449139,181449668,
slc16a1.SNM_001086927chr2+1998339371998416601998339371998416605199833937,199837146,199838682,199839032,199841514,199834154,199837290,199838921,199839528,199841660,
yipf5.SNM_001086926chr1+71644642716453917164464271645391471644642,71644906,71645093,71645325,71644870,71645089,71645325,71645391,
yipf5.SNM_001086926chr18-33285272332971023328527233297102533285272,33286582,33289507,33290876,33297033,33285425,33286765,33289654,33290972,33297102,
A630089N07RikNR_015491chr1-301121080546108054610805461630112,53098,53162,53221,69579,183734,183815,185513,361959,406602,716402,935918,1078494,1078992,1080165,1080417,30376,53108,53197,53230,69614,183802,184071,185642,362164,406650,716424,936128,1078573,1079031,1080226,1080546,
adss1.LNM_001096543chr13-938710249390011693871024939001161193871024,93875835,93877099,93878252,93879827,93882667,93883062,93887013,93888244,93889093,93900011,93871081,93875931,93877231,93878401,93879951,93882778,93883127,93887066,93888303,93889198,93900116,
NEK11NM_001146003chr8-11024984711051554911025048811051553011110249847,110250427,110333271,110356139,110407448,110411583,110422238,110423492,110435375,110451211,110515366,110249907,110250667,110333336,110356235,110407559,110411728,110422365,110423557,110435494,110451377,110515549,

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