Schema for xenoRefGene
  Database: apiMel2    Primary Table: xenoRefGene    Row Count: 99,689   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 674smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_004630varchar(255) values Name of gene (usually transcript_id from GTF)
chrom Group5varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 11671740int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 11675260int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 11671740int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 11675260int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 7int(10) unsigned range Number of exons
exonStarts 11671740,11672085,11672421,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 11671776,11672151,11672514,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 SF1varchar(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 0,0,0,0,0,1,0,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
        apiMel2.all_est.qName (via xenoRefGene.name)
      apiMel2.all_mrna.qName (via xenoRefGene.name)
      apiMel2.xenoMrna.qName (via xenoRefGene.name)
      apiMel2.xenoRefSeqAli.qName (via xenoRefGene.name)
      hgFixed.gbCdnaInfo.acc (via xenoRefGene.name)
      hgFixed.gbMiscDiff.acc (via xenoRefGene.name)
      hgFixed.gbWarn.acc (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
674NM_004630Group5-11671740116752601167174011675260711671740,11672085,11672421,11672603,11673114,11673310,11675181,11671776,11672151,11672514,11672762,11673219,11673450,11675260,0SF1incmplincmpl0,0,0,0,0,1,0,
586NM_004618Group14+19840520186219840520186210198405,198543,198803,198946,199209,199378,199594,199787,200021,201760,198504,198669,198873,199080,199290,199588,199669,199937,200270,201862,0TOP3Aincmplincmpl0,0,0,1,0,0,0,0,0,0,
718NM_001171247Group1+17453049174592301745304917459230517453049,17458494,17458593,17458726,17459023,17453115,17458560,17458629,17458789,17459230,0LOC100329104incmplincmpl0,0,0,0,0,
622NM_001002836Group10-494994749502534949947495025314949947,4950253,0ZNF787incmplincmpl0,
591NM_001042957Group11+90012790851290012790851215900127,900457,900770,901071,903420,903656,904012,904440,904972,905214,905499,905864,906160,906977,908401,900358,900577,900839,901155,903573,903866,904297,904752,905149,905427,905739,906050,906385,907070,908512,0Cht10incmplincmpl0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,
622NM_001164532Group10+488619848867594886198488675924886198,4886579,4886402,4886759,0Cpsf4lincmplincmpl0,0,
994NM_134368GroupUn+53727545537312285372754553731228753727545,53727772,53728702,53728972,53729749,53730307,53731096,53727696,53728071,53728861,53729725,53730289,53730619,53731228,0Smarca4incmplincmpl0,1,0,0,0,0,0,
604NM_176304Group10-255703425581432557034255814322557034,2558026,2557100,2558143,0Zasp66incmplincmpl0,0,
83NR_147785Group11+113997321142240011422400114224001111399732,11400074,11413899,11414147,11415765,11416865,11418760,11418838,11418943,11419307,11422304,11399960,11400077,11413992,11414264,11415771,11416946,11418823,11418892,11418990,11419443,11422400,0ARNTLunkunk-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
616NR_147180GroupUn-408552440922144092214409221454085524,4087652,4089776,4091128,4092124,4085605,4087784,4089893,4091269,4092214,0DTNBunkunk-1,-1,-1,-1,-1,

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