Schema for xenoRefGene
  Database: dp2    Primary Table: xenoRefGene    Row Count: 250,169   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 595smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001285470varchar(255) values Name of gene (usually transcript_id from GTF)
chrom Contig502_Contig4001varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1368451int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1396102int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1396102int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1396102int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 1368451,1394524,1395761,139...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1368487,1394551,1395772,139...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Steap2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-1,-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
        dp2.all_est.qName (via xenoRefGene.name)
      dp2.all_mrna.qName (via xenoRefGene.name)
      dp2.xenoMrna.qName (via xenoRefGene.name)
      dp2.xenoRefFlat.name (via xenoRefGene.name)
      dp2.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
595NM_001285470Contig502_Contig4001-136845113961021396102139610241368451,1394524,1395761,1396078,1368487,1394551,1395772,1396102,0Steap2unkunk-1,-1,-1,-1,
587NM_001165945Contig6581_Contig6381-3427653438963427653438962342765,343776,343125,343896,0CLCNKBincmplincmpl0,0,
587NM_001166044Contig2561_Contig6127+2683082694952683082694955268308,268476,268575,268699,268895,268377,268517,268669,268834,269495,0CDK9incmplincmpl0,0,2,0,0,
588NM_001192858Contig264_Contig4223-4466214474584466214474583446621,446684,447326,446675,446915,447458,0GALNT3incmplincmpl0,0,0,
590NM_001092387Contig2105_Contig7229-6894016900646894016900643689401,689647,689917,689608,689701,690064,0ddost.Sincmplincmpl0,0,0,
586NM_001102387Contig4092_Contig573-1666151669031666151669032166615,166771,166672,166903,0nox1incmplincmpl0,0,
596NM_001284365Contig446_Contig3289+154352615437121543526154371211543526,1543712,0ULK3incmplincmpl0,
585NM_165469Contig5727_Contig591-546995914554702590401754699,54870,55187,55581,55769,56039,56515,56657,56828,57160,58005,58260,58284,58553,58758,59001,59037,54804,55115,55525,55706,56030,56351,56651,56744,57107,57937,58216,58281,58499,58710,58905,59022,59145,0Pldcmplcmpl0,1,2,0,0,0,0,0,0,0,2,0,1,0,0,0,0,
585NM_165470Contig5727_Contig591-546995915154702590401754699,54870,55187,55581,55769,56039,56515,56657,56828,57160,58005,58260,58284,58553,58758,59001,59037,54804,55115,55525,55706,56030,56351,56651,56744,57107,57937,58216,58281,58499,58710,58905,59022,59151,0Pldcmplcmpl0,1,2,0,0,0,0,0,0,0,2,0,1,0,0,0,0,
585NM_165468Contig2917_Contig2974+6876468687646821687,936,1167,1314,2392,2623,3028,3211,3269,3634,3912,4170,4371,4797,4941,5061,5474,5691,5808,6011,6174,762,1017,1224,1428,2611,2965,3112,3243,3318,3694,4109,4284,4707,4833,5028,5339,5620,5808,6000,6131,6468,0bin3cmplcmpl0,0,0,0,0,0,0,0,1,0,1,0,0,0,0,0,1,0,0,2,0,

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