Schema for xenoRefGene
  Database: danRer3    Primary Table: xenoRefGene    Row Count: 569,447   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type description
bin 940smallint(5) unsigned Indexing field to speed chromosome range queries.
name NM_001256468varchar(255) Name of gene (usually transcript_id from GTF)
chrom chr19varchar(255) Reference sequence chromosome or scaffold
strand +char(1) + or - for strand
txStart 46614039int(10) unsigned Transcription start position (or end position for minus strand item)
txEnd 46620102int(10) unsigned Transcription end position (or start position for minus strand item)
cdsStart 46614039int(10) unsigned Coding region start (or end position for minus strand item)
cdsEnd 46620102int(10) unsigned Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned Number of exons
exonStarts 46614039,46614244,46620063,longblob Exon start positions (or end positions for minus strand item)
exonEnds 46614060,46614271,46620102,longblob Exon end positions (or start positions for minus strand item)
score 0int(11) score
name2 KAT6Bvarchar(255) Alternate name (e.g. gene_id from GTF)
cdsStartStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat incmplenum('none', 'unk', 'incmpl', 'cmpl') Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 1,1,1,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
        danRer3.all_est.qName (via xenoRefGene.name)
      danRer3.all_mrna.qName (via xenoRefGene.name)
      danRer3.refGene.name (via xenoRefGene.name)
      danRer3.refSeqAli.qName (via xenoRefGene.name)
      danRer3.xenoMrna.qName (via xenoRefGene.name)
      danRer3.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
940NM_001256468chr19+46614039466201024661403946620102346614039,46614244,46620063,46614060,46614271,46620102,0KAT6Bincmplincmpl1,1,1,
784NM_001256468chr9-261539352620110626153935262011032326153935,26154529,26154610,26154877,26155119,26155136,26155267,26155549,26157390,26157770,26158063,26158604,26160337,26161092,26 ...26154124,26154586,26154643,26154949,26155132,26155144,26155435,26155582,26157525,26157781,26158090,26158703,26160448,26161188,26 ...0KAT6Bcmplincmpl0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,2,0,0,1,0,2,0,0,
839NM_001266210chr14+33315297333193833331529733319383333315297,33316051,33319245,33315401,33316094,33319383,0CGRRF1cmplincmpl0,2,0,
653NM_001266198chr22+897293289739228972932897392228972932,8973823,8973142,8973922,0CCDC71incmplincmpl0,0,
99NM_001266208chr3-276292932766166727629293276616612127629293,27629856,27631152,27631320,27631523,27633913,27633932,27634285,27637681,27639447,27639629,27641868,27642085,27642350,27 ...27629376,27629911,27631221,27631442,27631644,27633916,27634020,27634365,27637780,27639540,27639861,27641966,27642268,27642488,27 ...0AP2A1cmplcmpl1,0,0,1,0,0,2,0,0,0,2,0,0,0,2,0,0,2,0,1,0,
2007NM_201271chrNA-1863851481863932161863851481863932162186385148,186393084,186385181,186393216,0Plppr1incmplcmpl0,0,
743NM_201269chrUn-20830110208400002083011020840000720830110,20830173,20837766,20838152,20839406,20839535,20839982,20830146,20830245,20837916,20838281,20839511,20839766,20840000,0ZNF644incmplincmpl0,0,0,0,0,0,0,
235NM_201636chrNA-1703928531704125911703928531704125916170392853,170405652,170405698,170405739,170405850,170412465,170392940,170405697,170405706,170405820,170405877,170412591,0TBXA2Rincmplincmpl0,0,1,0,0,0,
745NM_201637chr23+210260032107799821026003210779982521026003,21048774,21050441,21050894,21051102,21053443,21056092,21058144,21058473,21058746,21060407,21060817,21063248,21063787,21 ...21026108,21048884,21050451,21050975,21051204,21053562,21056333,21058147,21058650,21058890,21060665,21060974,21063442,21063940,21 ...0Chd8incmplincmpl0,0,2,0,0,0,2,0,0,0,0,0,1,0,0,0,0,0,1,0,0,2,0,0,0,
1026NM_001205605chrUn+578840555792143057884055579214301257884055,57895211,57905971,57908718,57910954,57911283,57915817,57916103,57917370,57921205,57921325,57921358,57884149,57895354,57906064,57908863,57911039,57911511,57916085,57916317,57917498,57921277,57921344,57921430,0PRKAA2cmplcmpl0,1,0,0,1,2,2,0,1,0,0,0,

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