Schema for xenoRefGene
  Database: calJac1    Primary Table: xenoRefGene    Row Count: 519,237   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 73smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001002980varchar(255) Name of gene (usually transcript_id from GTF)
chrom Contig1503varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 237242int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 264639int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 237242int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 264639int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 6int(10) unsigned Number of exons
exonStarts 237242,258325,258343,260897...longblob Exon start positions (or end positions for minus strand item)
exonEnds 237290,258343,258427,260927...longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 COL7A1varchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 2,0,0,0,0,0,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
        calJac1.all_est.qName (via xenoRefGene.name)
      calJac1.all_mrna.qName (via xenoRefGene.name)
      calJac1.refGene.name (via xenoRefGene.name)
      calJac1.refSeqAli.qName (via xenoRefGene.name)
      calJac1.xenoMrna.qName (via xenoRefGene.name)
      calJac1.xenoRefFlat.name (via xenoRefGene.name)
      calJac1.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_001002980Contig1503+2372422646392372422646396237242,258325,258343,260897,262440,264600,237290,258343,258427,260927,262470,264639,0COL7A1incmplincmpl2,0,0,0,0,0,
586NM_001170562Contig1316+1319061338581319061323025131906,132252,133480,133644,133716,132248,132303,133626,133659,133858,0Peg12incmplcmpl0,1,-1,-1,-1,
585NM_001109900Contig9753+52386737075238673694952386,55207,56240,57367,59465,62871,67099,69169,73662,52464,55376,56356,57445,59588,62983,67252,69238,73707,0Akr1c15cmplcmpl0,2,1,0,0,0,0,0,1,
73NM_001109888Contig104-24453536503624516036481722244535,244970,245160,246676,248435,248777,250523,251910,253574,257901,260349,260688,267731,268546,268740,270453,270620,271272,27 ...244580,244985,245307,246802,248557,248900,250658,252044,253665,258051,260485,260854,267849,268644,268777,270530,270711,271382,27 ...0Ptprccmplincmpl-1,-1,0,0,0,0,0,1,0,0,2,1,0,1,0,1,0,1,0,2,0,-1,
586NM_001374692Contig775-1719221720151720151720151171922,172015,0POMT1unkunk-1,
585NM_001354018Contig2132-273241162792732439246827324,38958,39204,107597,113108,113491,115572,116049,27554,39086,39246,107848,113246,113545,115963,116279,0NETO1incmplincmpl0,1,1,-1,-1,-1,-1,-1,
585NM_001166466Contig4641+539247155453924682192753924,58142,61872,67395,68026,68366,68479,68532,68721,68761,69059,69139,69157,69196,69264,69354,69696,70212,70276,70365,70418,70 ...54039,58364,61935,67531,68356,68410,68521,68659,68749,68822,69070,69148,69170,69211,69295,69366,69710,70249,70333,70395,70457,70 ...0Spock1incmplcmpl0,1,1,1,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
585NM_001271131Contig3659+70800711777080071169170800,71177,0Mrpl14incmplcmpl0,
587NM_001346628Contig1304-3532993537973532993537973353299,353488,353665,353383,353653,353797,0drn-1incmplincmpl0,0,0,
73NM_001313478Contig1306-3930128592239301285922339301,207097,285774,39346,207180,285922,0unc-75incmplincmpl0,1,0,

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