Schema for refGene
  Database: calJac1    Primary Table: refGene    Row Count: 263   Data last updated: 2020-08-20
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 596smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001204342varchar(255) values Name of gene (usually transcript_id from GTF)
chrom Contig22varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 1490260int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 1497443int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 1493264int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 1497443int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 1490260,1497194,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 1493501,1497443,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 TMED7varchar(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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 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
        calJac1.all_est.qName (via refGene.name)
      calJac1.all_mrna.qName (via refGene.name)
      calJac1.mrnaOrientInfo.name (via refGene.name)
      calJac1.refFlat.name (via refGene.name)
      calJac1.refSeqAli.qName (via refGene.name)
      calJac1.xenoMrna.qName (via refGene.name)
      calJac1.xenoRefGene.name (via refGene.name)
      calJac1.xenoRefSeqAli.qName (via refGene.name)
      hgFixed.gbCdnaInfo.acc (via refGene.name)
      hgFixed.gbMiscDiff.acc (via refGene.name)
      hgFixed.gbSeq.acc (via refGene.name)
      hgFixed.gbWarn.acc (via refGene.name)
      hgFixed.imageClone.acc (via refGene.name)
      hgFixed.refLink.mrnaAcc (via refGene.name)
      hgFixed.refSeqStatus.mrnaAcc (via refGene.name)
      hgFixed.refSeqSummary.mrnaAcc (via refGene.name)
      knownGeneV39.kgXref.refseq (via refGene.name)
      knownGeneV39.knownToRefSeq.value (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
596NM_001204342Contig22-149026014974431493264149744321490260,1497194,1493501,1497443,0TMED7cmplincmpl0,0,
585NM_001204437Contig16254-11167169241116716924511167,12626,15040,15380,16756,11345,12787,15190,15543,16924,0CYP2C8incmplcmpl0,1,1,0,0,
586NM_001204437Contig5417-1583101670651583101670654158310,160619,164007,166921,158492,160761,164195,167065,0CYP2C8cmplincmpl1,0,1,1,
594NM_001204434Contig72-126746012754431267808127458171267460,1270663,1271830,1272210,1272753,1273750,1275422,1268106,1270750,1271954,1272300,1272874,1274590,1275443,0CYP1A2cmplcmpl2,2,1,1,0,0,-1,
586NM_001204433Contig6300-1389661423961395871421952138966,142176,140681,142396,0P2RY11cmplcmpl1,0,
586NM_001204432Contig6300-14262914738614276514720212142629,143045,143285,143480,143636,143862,144169,145349,145622,145872,146925,147184,142968,143203,143415,143559,143760,143970,144246,145520,145673,145974,147096,147386,0PPANcmplcmpl1,2,1,0,2,2,0,0,0,0,0,0,
585NM_001257242Contig10466-18894350251889735013818894,19348,19666,22651,22917,24628,32485,34931,18911,19369,19783,22672,22938,24742,32833,35025,0MOGcmplcmpl1,1,1,1,1,1,1,0,
586NM_001257236Contig127-16225519930816227919506111162255,166462,167920,182746,185923,188137,188404,191808,192789,194979,199291,162366,166547,168017,182885,186069,188325,188558,191947,192935,195064,199308,0IL5RAcmplcmpl0,2,1,0,1,2,1,0,1,0,-1,
585NM_001257233Contig1311+82499844738249984473482499,82845,84140,84374,82643,82878,84269,84473,0IL5cmplcmpl0,0,0,0,
585NM_001257232Contig10241+34716597003473859669934716,37075,39504,43080,49055,52384,55109,56627,58093,34808,37214,39656,43232,49212,52484,55188,56677,59700,0IL4Rcmplcmpl0,1,2,1,0,1,2,0,2,

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