Schema for xenoRefGene
  Database: chlSab2    Primary Table: xenoRefGene    Row Count: 265,464   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 116smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001220482varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr26varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 45842614int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 46056143int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 45844460int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 46053172int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 45842614,45844326,45845717,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 45843024,45844472,45845950,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 MEIS2varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat cmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,0,0,2,0,0,0,0,1,0,2,1,1,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
        chlSab2.all_est.qName (via xenoRefGene.name)
      chlSab2.all_mrna.qName (via xenoRefGene.name)
      chlSab2.xenoRefFlat.name (via xenoRefGene.name)
      chlSab2.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
116NM_001220482chr26+458426144605614345844460460531721345842614,45844326,45845717,45847487,45848308,45849332,45850173,45859977,45907978,45994788,46048636,46050104,46052885,45843024,45844472,45845950,45847629,45848359,45849383,45850323,45860092,45908124,45994865,46048695,46050194,46056143,0MEIS2cmplcmpl-1,0,0,2,0,0,0,0,1,0,2,1,1,
939NM_012196chrX+46458496464700324645960046469980546458496,46459592,46460153,46467432,46469975,46458560,46459679,46460280,46467496,46470032,0GAGE8cmplcmpl-1,0,2,0,1,
1076NM_012205chr14+644606976448572964460744644853781064460697,64464375,64469097,64469622,64482226,64482625,64482967,64484887,64485138,64485299,64460824,64464454,64469181,64469726,64482319,64482669,64483113,64484956,64485221,64485729,0HAAOcmplcmpl0,2,0,0,2,2,1,0,0,2,
622NR_135644chr16+487997348809504880950488095054879973,4880313,4880494,4880671,4880774,4880018,4880316,4880575,4880757,4880950,0DHX33-DTunkunk-1,-1,-1,-1,-1,
825NM_001199355chr18+31473935314860603147394831483700831473935,31474076,31474883,31475262,31476241,31483520,31484848,31485255,31473988,31474117,31475018,31475361,31476433,31483703,31485213,31486060,0RPL17-C18orf32cmplcmpl0,1,0,0,0,0,-1,-1,
1067NM_001199354chr1+63293616633007596329367563299844563293616,63298143,63299271,63299702,63300599,63293757,63298349,63299420,63299990,63300759,0LRTOMTcmplcmpl0,1,0,2,-1,
13NM_001173463chr11-355525823570885235553795357087063735552582,35553127,35560084,35561584,35570048,35573228,35575194,35577003,35583624,35585158,35587907,35590745,35591169,35595984,35 ...35553091,35553889,35560284,35561755,35570166,35573396,35575372,35577140,35583753,35585266,35588127,35590795,35591230,35596150,35 ...0KIF21Acmplcmpl-1,2,0,0,2,2,1,2,2,2,1,2,1,0,0,2,0,2,0,0,0,1,1,0,0,0,0,1,0,2,0,0,0,0,0,2,0,
83NM_001039959chr1+11352870114589381136422811458651611352870,11363796,11364228,11365145,11458640,11458914,11353021,11363858,11364385,11365333,11458856,11458938,0Ahnakcmplcmpl-1,-1,0,1,1,-1,
84NM_001164559chr6-117864831179896211786483117986161711786483,11786661,11788006,11788175,11788394,11788542,11788803,11794337,11794528,11797511,11797858,11797936,11798228,11798375,11 ...11786561,11786770,11788092,11788310,11788466,11788629,11788923,11794450,11794644,11797699,11797918,11798001,11798282,11798494,11 ...0Trmt1incmplincmpl0,2,0,0,0,0,0,1,2,0,0,1,1,2,1,0,-1,
125NM_001246680chr24-547691685487694554769339548768071354769168,54769320,54775623,54779101,54811060,54814294,54816039,54821129,54834185,54847643,54857157,54876681,54876885,54769303,54769460,54775752,54779237,54811187,54814514,54816145,54821255,54834334,54847798,54857352,54876832,54876945,0Sptlc2cmplcmpl-1,2,2,1,0,2,1,1,2,0,0,0,-1,

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