Schema for xenoRefGene
  Database: panTro1    Primary Table: xenoRefGene    Row Count: 508,887   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 1277smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001043999varchar(255) Name of gene (usually transcript_id from GTF)
chrom chr8varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 90816628int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 90817306int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 90816628int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 90817306int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned Number of exons
exonStarts 90816628,90817177,longblob Exon start positions (or end positions for minus strand item)
exonEnds 90816685,90817306,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 Bcpvarchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        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)
      panTro1.all_est.qName (via xenoRefGene.name)
      panTro1.all_mrna.qName (via xenoRefGene.name)
      panTro1.refGene.name (via xenoRefGene.name)
      panTro1.refSeqAli.qName (via xenoRefGene.name)
      panTro1.xenoMrna.qName (via xenoRefGene.name)
      panTro1.xenoRefFlat.name (via xenoRefGene.name)
      panTro1.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1277NM_001043999chr8-90816628908173069081662890817306290816628,90817177,90816685,90817306,0Bcpincmplincmpl0,0,
11NM_001040678chr1+230050782333816923005078233381691023005078,23005318,23005437,23005608,23292350,23333617,23334367,23335575,23336639,23338021,23005285,23005437,23005590,23005701,23292401,23333728,23334574,23335779,23336785,23338169,0EPHA2incmplincmpl0,0,0,0,0,0,0,0,0,2,
858NR_112148chr18+35899698359006313590063135900631335899698,35900262,35900604,35899725,35900364,35900631,0unkunk-1,-1,-1,
672NM_001079969chr13_random+114614971148033811461515114803381111461497,11461745,11462164,11463818,11470258,11470518,11472055,11475966,11476197,11476875,11480197,11461557,11461867,11462316,11463946,11470436,11470574,11472176,11476108,11476254,11476879,11480338,0spoplbcmplcmpl0,0,2,1,0,1,0,1,2,2,0,
1152NM_001091116chr19+743460067435956874346006743595682874346006,74348099,74348894,74349427,74349730,74350389,74350860,74351200,74351458,74351903,74351969,74352668,74353203,74353644,74 ...74346126,74348264,74349047,74349514,74349817,74350506,74350910,74351309,74351542,74351915,74352035,74352947,74353258,74353747,74 ...0tmem94.Lincmplcmpl0,0,0,0,0,0,0,2,0,0,0,0,0,2,0,0,0,1,0,0,0,0,0,0,0,0,0,0,
167NM_001048096chr1+990782399914893299078765991488533599078239,99078697,99088500,99089254,99091421,99097490,99097850,99101781,99102235,99102439,99103540,99104721,99107009,99107718,99 ...99078341,99078847,99088711,99089423,99091623,99097672,99097961,99101892,99102338,99102537,99103678,99104911,99107133,99107882,99 ...0AGLcmplcmpl-1,0,1,2,0,1,2,2,2,0,2,2,0,1,0,0,0,1,0,2,1,1,0,2,1,2,0,1,2,1,0,1,0,2,-1,
1126NM_001303407chr18+70914152709142557091425570914255170914152,70914255,0CWF19L1unkunk-1,
1376NM_001303407chr8-10372542310376084610372635210374007515103725423,103725838,103726306,103728789,103729971,103731143,103736843,103738943,103739961,103743414,103746629,103753415,10375416 ...103725540,103725988,103726497,103728887,103730091,103731353,103736923,103739058,103740102,103743499,103746748,103753517,10375422 ...0CWF19L1cmplcmpl-1,-1,2,0,0,0,1,0,0,-1,-1,-1,-1,-1,-1,
2029NM_006613chr1+1893484811893497331893484811893488372189348481,189348758,189348757,189349733,0GRAPincmplcmpl2,2,
732NM_006613chr19-19303326193331971930476719333166419303326,19304156,19327758,19333088,19303935,19304959,19327859,19333197,0GRAPcmplcmpl-1,0,0,0,

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