Schema for xenoRefGene
  Database: canFam5    Primary Table: xenoRefGene    Row Count: 234,749   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 73smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001308327varchar(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 93123int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 167332int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 97460int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 167026int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 28int(10) unsigned range Number of exons
exonStarts 93123,94825,96957,97331,973...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 93165,94838,96980,97344,973...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Enpp1varchar(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 cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-1,-1,0,2,1,2,0,1,...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
        canFam5.all_est.qName (via xenoRefGene.name)
      canFam5.all_mrna.qName (via xenoRefGene.name)
      canFam5.refGene.name (via xenoRefGene.name)
      canFam5.refSeqAli.qName (via xenoRefGene.name)
      canFam5.xenoMrna.qName (via xenoRefGene.name)
      canFam5.xenoRefFlat.name (via xenoRefGene.name)
      canFam5.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
73NM_001308327chr1-93123167332974601670262893123,94825,96957,97331,97357,97460,99623,101264,102228,106896,111571,113315,114130,115550,118626,121000,123329,123710,124675,12 ...93165,94838,96980,97344,97375,97631,99696,101397,102308,107027,111693,113403,114200,115678,118764,121109,123400,123774,124788,12 ...0Enpp1incmplcmpl-1,-1,-1,-1,-1,0,2,1,2,0,1,0,2,0,2,1,2,1,2,0,1,2,0,0,1,0,0,-1,
73NM_001308329chr1-93123167332974601237172893123,94825,96957,97331,97357,97460,99623,101264,102228,106896,111571,113315,114130,115550,118626,121000,123329,123710,124675,12 ...93165,94838,96980,97344,97375,97631,99696,101397,102308,107027,111693,113403,114200,115678,118764,121109,123374,123774,124788,12 ...0Enpp1cmplcmpl-1,-1,-1,-1,-1,0,2,1,2,0,1,0,2,0,2,1,1,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
73NM_008813chr1-93123167332974601670262893123,94825,96957,97331,97357,97460,99623,101264,102228,106896,111571,113315,114130,115550,118626,121000,123329,123710,124675,12 ...93165,94838,96980,97344,97375,97631,99696,101397,102308,107027,111693,113403,114200,115678,118764,121109,123400,123774,124788,12 ...0Enpp1incmplcmpl-1,-1,-1,-1,-1,0,2,1,2,0,1,0,2,0,2,1,2,1,2,0,1,2,0,0,1,0,0,-1,
73NM_006208chr1-93473167141974601671314093473,93751,93856,93948,93970,94090,94818,94891,96494,96614,96664,96871,96944,97101,97283,97460,99533,101259,102228,106898,10858 ...93554,93778,93882,93959,94022,94159,94859,94936,96536,96624,96715,96882,97003,97197,97295,97631,99689,101397,102309,107027,10874 ...0ENPP1cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,1,1,0,1,1,1,0,2,1,1,0,2,2,0,0,1,2,0,1,1,0,0,0,
73NM_001206212chr1-97078167125974601671252597078,97460,99535,101264,102228,106897,108589,110642,111522,113315,114130,115550,118626,120998,123327,123710,124679,125852,12697 ...97196,97632,99696,101397,102309,107027,108736,110693,111693,113403,114200,115683,118762,121107,123400,123776,124787,125972,12705 ...0ENPP1incmplcmpl-1,2,2,1,1,0,2,1,1,0,2,1,1,0,2,2,0,0,1,2,1,1,1,0,0,
73NM_053535chr1-97460167122974601671222597460,99623,101264,102228,106896,108601,111571,113315,114130,115550,118631,121000,123329,123710,124675,125853,126976,128838,1289 ...97631,99696,101397,102308,107027,108724,111693,113403,114200,115683,118764,121109,123400,123774,124788,125972,127053,128843,1290 ...0Enpp1incmplcmpl0,2,1,2,0,0,1,0,2,1,2,1,2,1,2,0,1,2,2,0,0,1,0,0,0,
73NM_001168933chr1-97460167125974601671252497460,99535,101259,102228,106898,108589,110642,111523,113315,114130,115550,118626,120998,123327,123710,124677,125852,126976,1289 ...97631,99689,101397,102309,107027,108744,110693,111693,113403,114200,115683,118762,121107,123400,123776,124787,125972,127056,1290 ...0ENPP1incmplcmpl0,0,1,1,0,1,1,1,0,2,1,1,0,2,2,0,0,1,2,0,1,1,0,0,
73NM_001082742chr1-97460167156974601671562497460,99533,101268,102228,106897,108589,111523,113315,114132,115545,115549,118626,120998,123327,123710,124677,125852,126976,1289 ...97631,99698,101397,102309,107027,108745,111693,113405,114197,115547,115683,118762,121107,123400,123776,124787,125972,127056,1290 ...0ENPP1incmplcmpl0,0,1,1,0,0,1,1,2,0,1,1,0,2,2,0,0,1,0,0,1,1,0,2,
73NM_001030168chr1-10860413206110860413206113108604,111595,113315,114132,115525,115549,120996,122860,123332,124697,126976,128958,131932,108649,111693,113405,114196,115528,115678,121107,122865,123402,124760,127051,129048,132061,0enpp1incmplincmpl0,1,1,0,0,0,0,1,0,0,0,0,0,
73NM_001265722chr1+3384026541076116316541078338402,338848,611631,617809,625693,630569,644392,653899,338408,338885,611834,617943,625737,630574,644614,654107,0SLC66A2cmplcmpl-1,-1,0,2,1,0,2,2,

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