Schema for xenoRefGene
  Database: echTel2    Primary Table: xenoRefGene    Row Count: 470,748   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 596smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001275914varchar(255) values Name of gene (usually transcript_id from GTF)
chrom JH980389varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1459395int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1459500int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1459395int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1459500int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 1459395,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1459500,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Octbeta1Rvarchar(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,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
        echTel2.xenoRefFlat.name (via xenoRefGene.name)
      echTel2.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
596NM_001275914JH980389-145939514595001459395145950011459395,1459500,0Octbeta1Rincmplincmpl0,
708NM_001276014JH980313-16239685162401681623968516240168216239685,16240063,16240030,16240168,0Ythdfincmplincmpl0,0,
590NM_001276014JH980408+6554496559026554496559022655449,655587,655557,655902,0Ythdfincmplincmpl0,0,
597NM_001037787JH980390-167758916835541677589168355421677589,1683477,1677704,1683554,0Polr1dincmplincmpl2,0,
617NM_001043263JH980373-421675642972744216756429727454216756,4245486,4250012,4272121,4297202,4216870,4245612,4250165,4272232,4297274,0Dysincmplincmpl0,0,0,0,0,
903NM_001102030JH980305-41762665417631374176266541763137241762665,41763035,41762701,41763137,0LOC515697incmplincmpl0,0,
621NM_001098661JH980319+4811048482802348110484828023124811048,4817083,4824583,4825809,4826203,4826419,4826633,4826848,4827189,4827353,4827757,4827873,4811099,4817155,4824676,4825933,4826322,4826533,4826753,4827061,4827192,4827530,4827760,4828023,0LOC100049642cmplincmpl0,0,0,0,1,0,0,0,0,0,0,0,
721NM_001256179JH980297-17888297178999311788829717899931417888297,17896828,17897274,17899834,17888366,17896868,17897338,17899931,0mbipincmplincmpl0,2,1,0,
782NM_001271629JH980321+25938976259391522593915225939152225938976,25939125,25939055,25939152,0MEF2Dunkunk-1,-1,
585NM_001271629JH980333-1183401190521183401190524118340,118924,118954,119037,118400,118933,118974,119052,0MEF2Dincmplincmpl2,2,0,0,

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