Schema for xenoRefGene
  Database: ci3    Primary Table: xenoRefGene    Row Count: 84,144   Data last updated: 2017-04-25
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001102430varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 38483int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 57000int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 38483int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 57000int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 25int(10) unsigned range Number of exons
exonStarts 38483,39123,40396,40832,415...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 38563,39199,40477,40997,417...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Arfgef1varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 1,0,0,0,0,0,0,0,0,0,0,1,0,0...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
        ci3.all_est.qName (via xenoRefGene.name)
      ci3.all_mrna.qName (via xenoRefGene.name)
      ci3.refGene.name (via xenoRefGene.name)
      ci3.refSeqAli.qName (via xenoRefGene.name)
      ci3.xenoRefFlat.name (via xenoRefGene.name)
      ci3.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
585NM_001102430chr1-384835700038483570002538483,39123,40396,40832,41540,41952,42043,42572,43024,43534,43943,44307,44815,46194,46825,47636,48175,50685,51217,51221,51904,52 ...38563,39199,40477,40997,41711,42012,42054,42683,43243,43675,44042,44363,44984,46302,46967,47710,48337,50877,51220,51353,52002,52 ...0Arfgef1incmplincmpl1,0,0,0,0,0,0,0,0,0,0,1,0,0,2,0,0,0,0,0,1,0,0,0,0,
587NM_001084884chrUn_NW_004190356v1-3402443423043402443423046340244,340584,340945,341301,341745,342207,340366,340815,341170,341529,341976,342304,0UBQ10incmplincmpl1,1,1,1,1,0,
586NM_001085030chr9+1679491698271688061698274167949,168779,169191,169725,167991,168866,169311,169827,0GB2cmplincmpl-1,0,0,0,
606NM_001084918chr3+287652528782562876525287825652876525,2877072,2877691,2877920,2878215,2876720,2877192,2877796,2877999,2878256,0HOG1incmplincmpl0,0,0,0,1,
606NM_001084918chr8-281985128224052819851282240522819851,2822309,2820001,2822405,0HOG1incmplincmpl0,0,
603NM_001084909chr7-236812523687382368125236873832368125,2368281,2368672,2368209,2368359,2368738,0T20K18.140; T20K18_140incmplincmpl0,0,0,
585NM_001085006chrUn_NW_004190445v1-65225662026522566154465225,65565,65918,66109,65297,65687,66009,66202,0RPS6cmplincmpl0,1,0,0,
609NM_001287089chr3+321300332183153213003321831553213003,3215569,3216042,3216381,3218123,3213174,3215683,3216189,3216522,3218315,0ALDH1A2incmplincmpl0,0,0,0,0,
595NM_001287089chr4-132574113294501325741132945081325741,1326498,1327119,1327604,1327851,1328238,1328570,1329336,1325801,1326657,1327170,1327624,1327862,1328406,1328702,1329450,0ALDH1A2incmplincmpl0,0,0,0,0,0,0,0,
597NM_139068chr14-164826616517871648266165178761648266,1648440,1648671,1650166,1650889,1651697,1648356,1648482,1648830,1650391,1651123,1651787,0MAPK9incmplincmpl0,0,0,0,0,0,

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