Schema for xenoRefGene
  Database: ailMel1    Primary Table: xenoRefGene    Row Count: 402,766   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 594smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001104905varchar(255) values Name of gene (usually transcript_id from GTF)
chrom GL192614.1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1284394int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1286811int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1284394int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1286811int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 1284394,1286724,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1284538,1286811,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 st8sia6varchar(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 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
        ailMel1.all_est.qName (via xenoRefGene.name)
      ailMel1.all_mrna.qName (via xenoRefGene.name)
      ailMel1.xenoMrna.qName (via xenoRefGene.name)
      ailMel1.xenoRefFlat.name (via xenoRefGene.name)
      ailMel1.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
594NM_001104905GL192614.1-128439412868111284394128681121284394,1286724,1284538,1286811,0st8sia6incmplincmpl0,0,
73NM_001094894GL192539.1+1417003784681417003784499141700,174093,202462,205020,210029,238964,260368,263333,378317,141775,174216,202519,205026,210089,239144,260477,263440,378468,0elp4.Sincmplcmpl0,0,0,0,0,0,0,1,0,
585NM_001105004GL192348.1+81595860978162285886581595,81815,85466,85817,85995,81696,81957,85520,85981,86097,0FAM32Acmplcmpl0,2,0,0,-1,
592NM_001105004GL192488.1-92010192128492096492128414920101,920309,920357,920496,920523,920715,920776,920964,920989,921034,921066,921128,921147,921182,920132,920330,920441,920514,920666,920747,920881,920986,921034,921066,921090,921140,921179,921284,0FAM32Acmplincmpl-1,-1,-1,-1,-1,-1,-1,0,0,1,1,1,2,0,
590NM_001287421GL192700.1-7209997212217209997212211720999,721221,0ZSCAN26incmplincmpl0,
591NM_001287421GL193124.1+8211458212928211458212921821145,821292,0ZSCAN26incmplincmpl0,
73NM_001305422GL192908.1+39256944809939257444759713392569,412396,426654,428538,440585,441565,444158,446270,447533,447660,447769,447973,448039,392709,412537,426785,428645,440750,441728,444263,446426,447602,447744,447885,448023,448099,0RMND5Acmplcmpl0,0,0,2,1,1,2,2,2,-1,-1,-1,-1,
75NM_001321627GL192445.1-2316254239668123235272358633522316254,2316380,2316793,2317191,2317223,2317299,2317453,2317675,2317963,2318199,2318266,2318335,2318529,2318635,2318748,2318876, ...2316356,2316762,2317033,2317209,2317271,2317372,2317528,2317902,2318189,2318249,2318306,2318438,2318554,2318709,2318844,2319013, ...0FAM126Bcmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,1,1,0,2,2,2,0,0 ...
588NM_001317385GL193357.1-5078455085825080675085823507845,508067,508138,507902,508133,508582,0Prdx2incmplincmpl-1,0,0,
618NM_001317384GL192346.1-4428257444087744322964440765264428257,4428665,4428783,4428966,4429106,4429302,4429361,4429516,4429641,4430009,4430239,4430459,4430611,4430714,4430916,4430959, ...4428606,4428762,4428906,4428987,4429140,4429339,4429424,4429587,4429997,4430164,4430392,4430497,4430642,4430861,4430941,4431022, ...0AQP4cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,0,0,0,2,0,

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