Schema for xenoRefGene
  Database: geoFor1    Primary Table: xenoRefGene    Row Count: 378,647   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 74smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001384935varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JH739963varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 1780997int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1880108int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1781002int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1880108int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 1780997,1781914,1783232,179...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1781075,1781971,1783430,179...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 BANPvarchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,0,0,1,0,2,0,0,0,longblob   Reading frame of the start of the CDS region of the exon, in the direction of transcription (0,1,2), or -1 if there is no CDS region.

Connected Tables and Joining Fields
        geoFor1.all_mrna.qName (via xenoRefGene.name)
      geoFor1.xenoRefFlat.name (via xenoRefGene.name)
      geoFor1.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbSeq.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)
      hgFixed.imageClone.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
74NM_001384935JH739963+1780997188010817810021880108111780997,1781914,1783232,1796569,1798219,1806784,1820072,1826126,1828243,1875966,1880048,1781075,1781971,1783430,1796626,1798394,1807026,1820150,1826208,1828308,1876104,1880108,0BANPcmplcmpl0,0,0,0,0,1,0,2,0,0,0,
594NM_001097758JH740070+120262512033221202625120332231202625,1202667,1203232,1202643,1202718,1203322,0ca12.Lincmplincmpl0,0,0,
74NM_001097757JH739966-196027719667791960283196677941960277,1962714,1964478,1966697,1960442,1962756,1964591,1966779,0bloc1s5.Lincmplcmpl0,0,1,0,
598NM_001167678JH739943-175989117607871760691176078721759891,1760691,1759909,1760787,0znf706incmplcmpl-1,0,
585NM_001126596JH739958+32682328383268232838132682,32838,0tekt4incmplincmpl0,
591NM_001164497JH740005+85829687803685829687534622858296,863559,866354,867182,869259,870649,871218,871449,873042,875163,875365,875606,875849,875888,876100,877395,877484,877562,87 ...858416,863601,866470,867285,869379,870863,871345,871555,873234,875348,875392,875637,875873,876009,876134,877410,877507,877619,87 ...0Tent4bincmplcmpl0,0,0,2,0,0,1,2,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
604NM_001164496JH739910-2529130255496625291302554966122529130,2529239,2531042,2539668,2540176,2544964,2545072,2546819,2549054,2551615,2553163,2554945,2529145,2529323,2531207,2539721,2540303,2545057,2545172,2546911,2549090,2551733,2553378,2554966,0CFAP44incmplincmpl1,0,0,1,0,0,2,0,0,2,0,0,
592NM_001315606JH739918-9565379597679565379597678956537,956937,957386,957824,958235,958605,958654,959641,956644,957179,957632,957928,958530,958607,958834,959767,0LOC106371602incmplincmpl1,2,2,0,2,0,0,0,
585NM_001106410JH740614+14410209051446520905414410,19384,19975,20836,14478,19522,20180,20905,0Gpbp1cmplincmpl0,0,0,0,
587NM_001137609JH740188-30642332745130642932745114306423,309655,309662,311875,313335,315529,317310,319057,321184,322751,322994,323956,324176,327385,306497,309656,309791,311974,313446,315685,317335,319153,321385,322862,323138,324060,324249,327451,0TXNRD1incmplcmpl1,0,0,0,0,0,1,0,0,0,0,1,0,0,

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