Schema for xenoRefGene
  Database: hetGla2    Primary Table: xenoRefGene    Row Count: 536,763   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 588smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001107870varchar(255) Name of gene (usually transcript_id from GTF)
chrom JH602075varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 417271int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 429741int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 417521int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 429721int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 16int(10) unsigned Number of exons
exonStarts 417271,417378,417473,417608...longblob Exon start positions (or end positions for minus strand item)
exonEnds 417352,417429,417563,417681...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 Smyd5varchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('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 -1,-1,0,2,0,0,0,2,2,0,0,2,0...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
        hetGla2.xenoMrna.qName (via xenoRefGene.name)
      hetGla2.xenoRefFlat.name (via xenoRefGene.name)
      hetGla2.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
588NM_001107870JH602075-41727142974141752142972116417271,417378,417473,417608,417772,418556,419661,420113,420534,420826,421675,422334,422869,423456,424100,429625,417352,417429,417563,417681,417840,418649,419718,420220,420609,420885,421780,422404,422991,423596,424209,429741,0Smyd5cmplcmpl-1,-1,0,2,0,0,0,2,2,0,0,2,0,1,0,0,
586NM_001193325JH602174+1477311895301477311895308147731,166749,169556,177437,178907,182426,185537,189440,147803,166792,169651,177531,179083,182597,185681,189530,0fbxo25cmplcmpl0,0,1,0,1,0,0,0,
613NM_001271103JH602089+373422037349783734978373497893734220,3734259,3734340,3734368,3734500,3734601,3734648,3734792,3734887,3734235,3734288,3734355,3734487,3734589,3734626,3734685,3734816,3734978,0Ncor1unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,
77NM_001271103JH602190+4203089437806642332814377211524203089,4203155,4233211,4242829,4242892,4250725,4256915,4266025,4270941,4271733,4274187,4276693,4278294,4283308,4284253,4285284, ...4203116,4203257,4233389,4242892,4242957,4250918,4257098,4266139,4270998,4271786,4274254,4276866,4278385,4283487,4284308,4285386, ...0Ncor1cmplcmpl-1,-1,0,0,0,2,0,0,0,0,2,0,2,0,2,0,0,0,1,1,1,1,0,1,1,0,1,0,1,0,2,1,1,1,0,0,2,1,1,0,0,2,2,1,0,1,1,-1,-1,-1,-1,-1,
726NM_001284721JH602059-18505936185251891850632918511673518505936,18508348,18508532,18511574,18525138,18506443,18508447,18508604,18511702,18525189,0NUTF2cmplcmpl0,0,0,0,-1,
85NM_001173054JH602052-129418761298749412942164129874831612941876,12941953,12945538,12946481,12949119,12951294,12951512,12952025,12954180,12954965,12954996,12960567,12965039,12965128,12 ...12941939,12942311,12946477,12946778,12949261,12951399,12951515,12952229,12954314,12954996,12955083,12960657,12965128,12965140,12 ...0Ahrcmplcmpl-1,0,0,0,1,0,0,0,1,0,0,0,1,1,2,0,
771NM_001193317JH602047+244355662446476624438494244639232824435566,24438482,24439941,24442483,24443668,24444061,24446133,24448151,24448867,24449350,24450927,24454241,24456120,24456636,24 ...24435626,24438587,24440044,24442630,24443707,24444124,24446191,24448244,24448901,24449453,24450952,24454318,24456196,24456771,24 ...0VIPAS39cmplcmpl-1,0,0,1,1,2,2,0,0,1,2,0,2,0,0,0,0,0,0,0,-1,-1,-1,-1,-1,-1,-1,-1,
594NM_001310374JH602083-125554612608721255546126087231255546,1258470,1260755,1255636,1258605,1260872,0TTRincmplincmpl0,0,0,
587NR_125733JH602059+3921923925653925653925652392192,392521,392236,392565,0TTTY14unkunk-1,-1,
595NM_001376461JH602080+1325528134489213255391339056351325528,1326473,1326899,1328352,1330698,1331550,1333576,1336260,1337118,1338342,1338928,1339181,1339609,1339809,1339838,1340019, ...1325717,1326556,1326948,1328487,1330778,1331712,1333652,1336371,1337304,1338486,1339094,1339473,1339745,1339823,1339883,1340043, ...0CELF1cmplcmpl0,1,0,1,1,0,0,1,1,1,1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,

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