Schema for xenoRefGene
  Database: mm10    Primary Table: xenoRefGene    Row Count: 193,238   Data last updated: 2020-08-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1022smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001164803varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 57385146int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 57392979int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 57385167int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 57391675int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 57385146,57385186,57388057,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 57385182,57385195,57388149,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 RBMXvarchar(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 0,0,1,1,0,1,0,-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
        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)
      mm10.all_est.qName (via xenoRefGene.name)
      mm10.all_mrna.qName (via xenoRefGene.name)
      mm10.refGene.name (via xenoRefGene.name)
      mm10.refSeqAli.qName (via xenoRefGene.name)
      mm10.xenoMrna.qName (via xenoRefGene.name)
      mm10.xenoRefFlat.name (via xenoRefGene.name)
      mm10.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
1022NM_001164803chrX-57385146573929795738516757391675857385146,57385186,57388057,57388527,57388744,57391271,57391566,57392958,57385182,57385195,57388149,57388647,57388859,57391378,57391685,57392979,0RBMXcmplcmpl0,0,1,1,0,1,0,-1,
846NM_001243962chr17+34263366342680463426336634268046534263366,34263424,34264757,34267338,34267922,34263397,34263429,34264996,34267615,34268046,0HLA-DQB1incmplincmpl1,2,1,1,1,
846NM_001243961chr17+34239043343151553423904334315155634239043,34241002,34264761,34267338,34314487,34315044,34239057,34241008,34265006,34267616,34314490,34315155,0HLA-DQB1incmplincmpl0,2,2,1,0,0,
16NM_001243960chr18+648878446521782664888047652128864664887844,64887990,64997347,65074723,65077697,65080017,65143791,65155255,65155643,65157844,65161514,65161654,65162988,65165571,65 ...64887928,64888095,64997421,65074805,65077736,65080067,65143846,65155315,65155748,65158011,65161635,65161660,65163171,65165646,65 ...0NEDD4Lcmplcmpl-1,0,0,2,0,0,2,0,0,0,2,0,0,0,0,0,0,0,1,0,0,2,0,0,0,2,0,0,0,1,2,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,
1850NM_001281769chr2-1658458191658848381658460081658846216165845819,165845900,165845964,165851999,165875704,165884607,165845849,165845917,165846239,165852148,165875775,165884838,0ZMYND8cmplcmpl-1,-1,0,1,2,0,
826NM_000972chr15-31654756316555693165476631655566231654756,31655430,31655430,31655569,0RPL7Acmplcmpl2,0,
799NM_001010996chr2-28076574280830032807657428083003628076574,28078249,28079121,28079621,28079905,28082912,28076825,28078381,28079251,28079754,28079934,28083003,0FCN1incmplcmpl1,1,0,2,0,2,
660NM_001001557chr4+9844354986220798444779860284129844354,9844440,9844728,9859332,9859829,9860952,9861376,9861644,9861792,9861816,9861879,9861907,9844431,9844579,9844890,9859829,9860297,9861061,9861568,9861716,9861802,9861858,9861888,9862207,0GDF6cmplcmpl-1,0,2,2,1,-1,-1,-1,-1,-1,-1,-1,
16NM_001044549chr10-607650336083121260765207608311651860765033,60765185,60766979,60768322,60769107,60772177,60772488,60773743,60774352,60774965,60777385,60778167,60778783,60779667,60 ...60765060,60765373,60767160,60768488,60769257,60772411,60772657,60773831,60774740,60775158,60777554,60778335,60778964,60779771,60 ...0UNC5Bcmplcmpl-1,2,1,0,0,0,2,1,0,0,1,1,0,1,0,1,1,0,
1731NM_001109908chr4+15023672915024887315023948115024855514150236729,150239475,150241044,150242121,150244004,150244240,150245114,150246569,150247450,150247830,150248060,150248485,15024860 ...150236890,150239566,150241140,150242180,150244074,150244374,150245337,150246767,150247652,150247939,150248119,150248591,15024881 ...0Eno1cmplcmpl-1,0,1,1,0,1,0,1,1,2,0,2,-1,-1,

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