Schema for xenoRefGene
  Database: dm6    Primary Table: xenoRefGene    Row Count: 55,280   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 811smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001191341varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr3Rvarchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 29684568int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 29685342int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 29684568int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 29685342int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 29684568,29684910,29685168,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 29684775,29685144,29685342,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 GUCY1A2varchar(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 0,0,0,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
        dm6.all_est.qName (via xenoRefGene.name)
      dm6.all_mrna.qName (via xenoRefGene.name)
      dm6.refGene.name (via xenoRefGene.name)
      dm6.refSeqAli.qName (via xenoRefGene.name)
      dm6.xenoMrna.qName (via xenoRefGene.name)
      dm6.xenoRefFlat.name (via xenoRefGene.name)
      dm6.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
811NM_001191341chr3R+29684568296853422968456829685342329684568,29684910,29685168,29684775,29685144,29685342,0GUCY1A2incmplincmpl0,0,0,
664NM_001201321chr2L+10427167104278091042717010427809410427167,10427386,10427497,10427698,10427363,10427473,10427668,10427809,0kdelr2acmplcmpl0,0,0,0,
749NM_001013463chr2L-21518108215184082151810821518408121518108,21518408,0zgc:114046incmplcmpl0,
810NM_001091717chr3R+29619581296205042961958129620504429619581,29619829,29619958,29620255,29619653,29619904,29620207,29620504,0slc25a11.Sincmplincmpl0,0,0,0,
667NM_001636chrX-10781620107826491078162010782649410781620,10781760,10782171,10782379,10781749,10782064,10782297,10782649,0SLC25A6incmplcmpl0,0,0,0,
748NM_178196chr2L-21472541214728942147259421472894221472541,21472594,21472559,21472894,0H2bc8incmplcmpl-1,0,
748NM_178196chr2L-21487778214881312148783121488131221487778,21487831,21487796,21488131,0H2bc8incmplcmpl-1,0,
701NM_001180289chr3R+15244374152455651524437415245565515244374,15244434,15244932,15245130,15245511,15244413,15244914,15245103,15245505,15245565,0SSB1incmplincmpl0,0,0,0,0,
718NM_001179279chr2R+17518290175189401751829017518940217518290,17518790,17518368,17518940,0IMP3cmplincmpl0,0,
738NM_001317022chr3R-20081346200823392008134620082339420081346,20081757,20081940,20082258,20081718,20081844,20082234,20082339,0LOC106719192incmplincmpl0,0,0,0,

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