Schema for xenoRefGene
  Database: manPen1    Primary Table: xenoRefGene    Row Count: 548,155   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 585smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001361676varchar(255) Name of gene (usually transcript_id from GTF)
chrom KN011312varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 1217int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 36104int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 1217int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 25321int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned Number of exons
exonStarts 1217,3173,6150,9227,11369,1...longblob Exon start positions (or end positions for minus strand item)
exonEnds 1301,3249,6285,9302,11483,1...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 Nf2varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 2,2,0,0,0,0,0,2,0,2,1,-1,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
        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)
      manPen1.xenoRefFlat.name (via xenoRefGene.name)
      manPen1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585NM_001361676KN011312+121736104121725321121217,3173,6150,9227,11369,14084,14940,16401,19699,21617,25283,36043,1301,3249,6285,9302,11483,14207,15158,16507,19827,21729,25330,36104,0Nf2incmplcmpl2,2,0,0,0,0,0,2,0,2,1,-1,
585NM_001257964KN018346-30081301983019830198130081,30198,0BOD1L2unkunk-1,
586NM_001257964KN006349+1393631403451403451403454139363,139433,139520,140279,139421,139473,139837,140345,0BOD1L2unkunk-1,-1,-1,-1,
585NM_001076835KN012584-117305933513163592942011730,12027,12223,12350,12449,12520,12633,12800,12859,12930,14736,16483,17565,28006,29799,33385,35816,36663,49417,59271,11951,12158,12336,12408,12485,12607,12789,12830,12908,13248,14843,16692,17699,28150,29983,33501,35911,36822,49991,59335,0KLHL20cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,2,0,1,2,2,1,2,0,0,2,0,
585NM_001105101KN006218-163935699163935699201639,2679,2939,3682,4165,5709,6553,7058,8045,8508,8636,11082,17706,17925,18577,20125,21107,23581,34886,35591,1698,2766,3020,3764,4261,5888,6679,7102,8141,8618,8675,11175,17710,18087,18657,20184,21228,23665,34997,35699,0ezh2incmplcmpl1,1,1,0,0,1,1,2,2,0,0,0,2,2,0,1,0,0,0,0,
585NR_029686KN011349-16052161381613816138116052,16138,0MIR145unkunk-1,
585NM_172696JPTV01131269-10572548910572548941057,10815,12879,25363,1195,10869,12963,25489,0Patjincmplincmpl0,0,0,0,
73NM_172696KN006129+89101511278910149213188910,29989,55129,92089,109969,114706,117153,118387,122931,128396,129252,141578,149185,149788,150735,150836,151010,151092,9105,30081,55204,92231,110053,114901,117300,118470,123034,128517,129359,141685,149341,149827,150786,150902,151021,151127,0Patjincmplcmpl0,0,2,2,0,0,0,0,2,0,1,0,2,-1,-1,-1,-1,-1,
586NM_001175815KN007654+1723611727541723611727542172361,172580,172460,172754,0LOC100383150incmplincmpl0,0,
585NM_001366285KN013225-24582393592458239359424582,28752,30429,39210,24645,28887,30694,39359,0TBXTincmplincmpl0,0,2,0,

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