Schema for xenoRefGene
  Database: mm8    Primary Table: xenoRefGene    Row Count: 193,643   Data last updated: 2020-08-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1322smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001206415varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr11varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 96605246int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 96622967int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 96616897int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 96622850int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 5int(10) unsigned range Number of exons
exonStarts 96605246,96616858,96617518,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 96605316,96617036,96617657,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 CBX1varchar(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 -1,0,2,1,2,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)
      mm8.all_est.qName (via xenoRefGene.name)
      mm8.all_mrna.qName (via xenoRefGene.name)
      mm8.refGene.name (via xenoRefGene.name)
      mm8.refSeqAli.qName (via xenoRefGene.name)
      mm8.xenoMrna.qName (via xenoRefGene.name)
      mm8.xenoRefFlat.name (via xenoRefGene.name)
      mm8.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1322NM_001206415chr11+96605246966229679661689796622850596605246,96616858,96617518,96618815,96622705,96605316,96617036,96617657,96618912,96622967,0CBX1cmplcmpl-1,0,2,1,2,
993NM_001312495chr18-53534487535369435353448753536943353534487,53536355,53536883,53534678,53536446,53536943,0LOC106114223incmplincmpl1,0,0,
1087NM_001312495chr9+65858382658636776585838265863677465858382,65859475,65860997,65863492,65858409,65859577,65861088,65863677,0LOC106114223incmplincmpl0,0,0,1,
1680NM_001015586chr2+1436298241436337341436298241436336773143629824,143631392,143633567,143630133,143631469,143633734,0DSTNincmplcmpl2,2,1,
995NM_165589chr14+53849052538513735384905253851373553849052,53849850,53850021,53851157,53851334,53849142,53849901,53850129,53851247,53851373,0Pabp2incmplincmpl0,0,0,0,0,
877NM_001078898chr19+383301223837195238330122383715991238330122,38330718,38349114,38349287,38363072,38365852,38366304,38370765,38371113,38371194,38371650,38371880,38330241,38330791,38349187,38349357,38363145,38366021,38366471,38371091,38371170,38371599,38371680,38371952,0lgi1incmplcmpl0,2,0,1,2,0,1,0,0,0,-1,-1,
181NM_001043528chr7-1138414891139086421138414891139086427113841489,113849546,113849717,113850110,113851399,113851512,113908576,113841591,113849552,113849831,113850208,113851401,113851600,113908642,0Ras2incmplincmpl0,0,0,0,1,0,0,
1417NM_001277210chr13+10916717010917050510916820810916880712109167170,109168191,109168783,109169040,109169107,109169343,109169555,109169761,109170052,109170173,109170233,109170414,109167314,109168409,109169030,109169098,109169327,109169503,109169698,109169958,109170147,109170206,109170275,109170505,0Smim15cmplcmpl-1,0,0,-1,-1,-1,-1,-1,-1,-1,-1,-1,
1266NM_002456chr3+89317018893190388931701889319025689317018,89317425,89317533,89317703,89317889,89318947,89317136,89317476,89317557,89317808,89318039,89319038,0MUC1incmplcmpl0,0,0,0,0,0,
1266NM_002455chr3-89295132893003358929513389300252989295132,89295426,89296033,89296192,89296507,89298609,89298803,89299739,89300152,89295343,89295586,89296110,89296372,89296603,89298689,89298873,89299932,89300335,0MTX1cmplcmpl0,2,0,0,0,1,0,2,0,

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