Schema for xenoRefGene
  Database: oryLat2    Primary Table: xenoRefGene    Row Count: 267,261   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 603smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001131178varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr8varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 2445974int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 2447149int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 2445980int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 2447129int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 2445974,2446100,2446285,244...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 2446025,2446202,2446450,244...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 EIF1varchar(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 0,0,0,0,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
        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)
      oryLat2.all_est.qName (via xenoRefGene.name)
      oryLat2.all_mrna.qName (via xenoRefGene.name)
      oryLat2.refGene.name (via xenoRefGene.name)
      oryLat2.refSeqAli.qName (via xenoRefGene.name)
      oryLat2.xenoMrna.qName (via xenoRefGene.name)
      oryLat2.xenoRefFlat.name (via xenoRefGene.name)
      oryLat2.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
603NM_001131178chr8-244597424471492445980244712942445974,2446100,2446285,2447100,2446025,2446202,2446450,2447149,0EIF1cmplcmpl0,0,0,0,
711NM_001172117chr22-16562411165780541656241116578054716562411,16562687,16562946,16573496,16576851,16577092,16577951,16562602,16562814,16563093,16573666,16576995,16577238,16578054,0Hckincmplincmpl1,0,0,0,0,1,0,
10NM_001256922chr23-10364892107668441036489210766844610364892,10545034,10545310,10764639,10764793,10766832,10364991,10545142,10545471,10764793,10764794,10766844,0ZNF70incmplincmpl0,0,1,0,2,2,
610NM_001256922ultracontig182+330753133206443307531332064433307531,3307882,3320482,3307636,3307936,3320644,0ZNF70incmplincmpl0,0,0,
736NM_001200413chr17-19909324199123281990932419912328419909324,19909546,19909702,19912124,19909474,19909599,19909838,19912328,0atpsckmtincmplincmpl0,1,0,0,
640NM_001200419chr20+723133772341877231337723399047231337,7232746,7233936,7234160,7231439,7232870,7233990,7234187,0klf6acmplcmpl0,0,0,-1,
704NM_001190419chr6-15683088156871581568309415687158915683088,15683863,15684997,15685170,15685344,15686381,15686580,15686867,15687062,15683309,15684077,15685087,15685261,15685507,15686473,15686691,15686964,15687158,0SEPHS1cmplcmpl1,0,0,2,0,1,1,0,0,
73NM_001200417chr12+5798499824325798495849807579849,580617,582811,584534,584704,584875,982390,579987,580710,582874,584612,584797,584980,982432,0pitpnblincmplincmpl0,0,0,0,0,0,-1,
679NM_001200417chr14+12345536123493051234553612349305612345536,12346824,12347667,12347821,12348811,12349181,12345671,12346920,12347736,12347893,12348898,12349305,0pitpnblincmplincmpl0,0,0,0,0,0,
719NM_001200417chr9-17668915176759591766891517675959817668915,17670120,17671858,17673843,17674019,17674311,17674605,17675932,17669032,17670201,17671936,17673879,17674082,17674405,17674748,17675959,0pitpnblincmplincmpl0,0,0,0,0,2,0,0,

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