Schema for xenoRefGene
  Database: mm39    Primary Table: xenoRefGene    Row Count: 197,343   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 76smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_052898varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 3270069int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 3742017int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3286244int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 3741571int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 59int(10) unsigned range Number of exons
exonStarts 3270069,3270271,3270366,327...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3270248,3270287,3270442,327...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 XKR4varchar(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,-1,-1,-1,-1,-1,-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
        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)
      mm39.all_est.qName (via xenoRefGene.name)
      mm39.all_mrna.qName (via xenoRefGene.name)
      mm39.refGene.name (via xenoRefGene.name)
      mm39.refSeqAli.qName (via xenoRefGene.name)
      mm39.xenoMrna.qName (via xenoRefGene.name)
      mm39.xenoRefFlat.name (via xenoRefGene.name)
      mm39.xenoRefSeqAli.qName (via xenoRefGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
76NM_052898chr1-3270069374201732862443741571593270069,3270271,3270366,3270659,3270864,3270930,3271359,3271862,3275217,3275445,3275507,3275526,3275685,3275814,3276161,3276401, ...3270248,3270287,3270442,3270746,3270888,3270993,3271428,3271922,3275286,3275494,3275517,3275634,3275711,3275896,3276172,3276414, ...0XKR4cmplcmpl-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1 ...
76NM_001011971chr1-3284702374263632862443742487133284702,3285201,3285877,3285914,3491924,3740774,3740924,3742103,3742184,3742242,3742378,3742432,3742450,3285161,3285677,3285901,3287191,3492124,3740878,3741190,3742179,3742242,3742371,3742432,3742449,3742636,0Xkr4cmplcmpl-1,-1,-1,1,2,0,0,2,1,0,0,1,0,
76NM_001033036chr1-328615737416693286244374157163286157,3491924,3740774,3740924,3741036,3741358,3287191,3492124,3740878,3741036,3741316,3741669,0XKR4cmplcmpl1,2,0,1,0,0,
76NM_001012258chr1-328618837415713286244374157183286188,3286244,3286622,3491924,3740769,3740929,3741045,3741460,3286209,3286526,3287191,3492119,3740857,3740956,3741304,3741571,0xkr4cmplcmpl-1,0,1,1,0,0,0,0,
76NM_001032714chr1-328624437415743286244374157173286244,3286622,3491922,3740774,3740929,3741036,3741460,3286505,3286835,3492124,3740851,3740956,3741310,3741574,0xkr4cmplcmpl0,0,2,0,0,0,0,
76NM_001032307chr1-328624437415753286244374157173286244,3491924,3740774,3740929,3741045,3741445,3741533,3287191,3492124,3740874,3740980,3741325,3741530,3741575,0xkr4cmplcmpl1,2,1,0,0,2,0,
613NM_001077752chr1-374077637415713740776374157143740776,3740929,3741045,3741460,3740857,3740956,3741304,3741571,0xkr4cmplincmpl0,0,0,0,
9NM_001375654chr1-4069791442306040697914423048314069791,4077944,4089292,4094958,4112141,4162839,4189890,4190237,4212834,4218034,4218832,4234077,4240427,4267808,4276882,4296834, ...4069842,4077960,4089371,4095115,4112330,4163003,4189935,4190296,4212989,4218184,4218967,4234164,4240601,4267864,4277060,4297050, ...0RP1cmplincmpl0,1,0,2,0,1,1,2,0,0,0,0,0,1,0,2,0,1,0,0,2,1,0,1,0,0,0,1,2,0,2,
618NM_001195676chr1-4414416443061544147734423048144414416,4414556,4414830,4416111,4417038,4417411,4417434,4417914,4419139,4419957,4420083,4422132,4422424,4430422,4414527,4414829,4416111,4417038,4417291,4417430,4417911,4419136,4419952,4420080,4420314,4422304,4423060,4430615,0Rp1cmplcmpl-1,1,0,1,0,2,1,0,0,1,0,0,0,-1,
618NM_001280013chr1-4414827442304844148274423048264414827,4415026,4415314,4416202,4416520,4416757,4417115,4417237,4417549,4418229,4418317,4418680,4418869,4418921,4418925,4419104, ...4414953,4415062,4416052,4416517,4416617,4416895,4417233,4417288,4418148,4418257,4418631,4418788,4418920,4418925,4419027,4419113, ...0RP1cmplincmpl1,0,0,0,2,0,1,0,1,0,1,0,1,2,1,1,1,1,0,0,0,1,2,0,1,0,

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