Schema for xenoRefGene
  Database: criGri1    Primary Table: xenoRefGene    Row Count: 552,644   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 586smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_194291varchar(255) Name of gene (usually transcript_id from GTF)
chrom KE377098varchar(255) Reference sequence chromosome or scaffold
strand -char(1) + or - for strand
txStart 244014int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 244784int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 244363int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 244784int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned Number of exons
exonStarts 244014,244106,244187,244206,longblob Exon start positions (or end positions for minus strand item)
exonEnds 244059,244173,244197,244784,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 TMEM65varchar(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 -1,-1,-1,2,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
        criGri1.all_est.qName (via xenoRefGene.name)
      criGri1.all_mrna.qName (via xenoRefGene.name)
      criGri1.refGene.name (via xenoRefGene.name)
      criGri1.refSeqAli.qName (via xenoRefGene.name)
      criGri1.xenoMrna.qName (via xenoRefGene.name)
      criGri1.xenoRefFlat.name (via xenoRefGene.name)
      criGri1.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
586NM_194291KE377098-2440142447842443632447844244014,244106,244187,244206,244059,244173,244197,244784,0TMEM65incmplcmpl-1,-1,-1,2,
589NM_001268772KE377556+6000906027876001686027873600090,600123,602739,600112,600225,602787,0unc-30cmplincmpl-1,0,0,
624NM_001353265KE382060+5158904520070351723905198622215158904,5172380,5179125,5184007,5188087,5189242,5190910,5191834,5192984,5194347,5198558,5198736,5199036,5199144,5199316,5199413, ...5158947,5172463,5179247,5184109,5188228,5189320,5191027,5191914,5193111,5194418,5198622,5199026,5199089,5199296,5199368,5199422, ...0CYRIBcmplcmpl-1,0,1,0,0,0,0,0,2,0,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
591NM_010750KE378856-8092578118848103678114476809257,809540,809611,810000,810210,811623,809527,809571,809991,810118,811606,811884,0Mab21l1cmplcmpl-1,-1,-1,-1,0,-1,
587NM_010751KE376559-33199935412033584335412022331999,332357,332472,332720,333097,333129,333494,333569,333628,333820,334119,334168,334225,334298,334447,334614,335839,336435,33 ...332338,332435,332707,333083,333120,333198,333548,333592,333810,333976,334137,334216,334246,334382,334577,335829,336004,336603,33 ...0Mxd1incmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,1,0,2,2,0,0,
586NM_001290825KE378452-15002419990515090619424367150024,150171,150297,150393,150425,150512,150657,150852,150880,151272,151440,151755,151847,152413,152537,152916,153566,153786,15 ...150125,150276,150357,150406,150461,150557,150815,150865,150961,151351,151498,151838,151891,152537,152765,153046,153677,153876,15 ...0Col17a1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,2,1,0,0,1,0,0,0,1,1,1,1,0,1,2,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,1,0,1,1,1,1,1,1,0,1,2,1,1,1,1,1,1,1,1,1,1,1, ...
585NR_002316AMDS01111072-68422884228842288418684,4657,6190,6219,7045,7793,9882,10243,11143,11566,18679,18882,19216,19810,19916,20260,20301,22872,702,4669,6204,6238,7060,7811,9892,10255,11155,11578,18700,18894,19228,19825,19929,20262,20320,22884,0CB741658unkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
590NM_001160555KE382394+7644407645487644407645481764440,764548,0hbb1incmplincmpl0,
594NM_001267038KE377948-118254312045891183661120458991182543,1183634,1187671,1192495,1194270,1194452,1200491,1201809,1204532,1182579,1183820,1187725,1192622,1194369,1194535,1200533,1201881,1204589,0CENPKincmplcmpl-1,0,0,2,2,0,0,0,0,
73NM_001285193KE383691+37666739651937674639494221376667,385472,386556,387298,390103,391686,392501,393122,393400,394645,394840,395065,395256,395460,395635,395734,395882,396023,39 ...376794,385536,386632,387424,390228,391903,392594,393299,393460,394687,395029,395167,395299,395484,395686,395785,396004,396072,39 ...0ACTR1Acmplcmpl0,0,2,0,0,2,0,0,0,0,0,-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.