Schema for refGene
  Database: canFam2    Primary Table: refGene    Row Count: 2,325   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 1053smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001048126varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr16varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 61341720int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 61394172int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 61342175int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 61394146int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 9int(10) unsigned range Number of exons
exonStarts 61341720,61345402,61349407,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 61342336,61345533,61349574,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ANGPT2varchar(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 1,2,0,0,1,2,0,0,0,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
        canFam2.all_est.qName (via refGene.name)
      canFam2.all_mrna.qName (via refGene.name)
      canFam2.refFlat.name (via refGene.name)
      canFam2.refSeqAli.qName (via refGene.name)
      canFam2.xenoMrna.qName (via refGene.name)
      canFam2.xenoRefGene.name (via refGene.name)
      canFam2.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
1053NM_001048126chr16-61341720613941726134217561394146961341720,61345402,61349407,61350118,61355583,61357594,61361603,61365316,61393861,61342336,61345533,61349574,61350220,61355714,61357827,61361725,61365472,61394172,0ANGPT2cmplcmpl1,2,0,0,1,2,0,0,0,
1504NM_001048125chrX-1205654811205859121205654811205859129120565481,120569490,120572468,120577623,120579301,120582017,120584400,120585222,120585815,120565972,120569664,120572595,120577794,120579502,120582106,120584578,120585359,120585912,0IDScmplcmpl1,1,0,0,0,1,0,1,0,
81NM_001048124chrX+928947193148799289559931387729289471,9310727,9289562,9314879,0TLR7cmplcmpl0,0,
596NM_001048123chrX+152159315403861521593154038691521593,1523176,1525641,1527856,1529661,1533795,1537127,1538287,1540018,1521685,1523298,1525767,1528280,1529802,1533926,1537290,1538409,1540386,0ARSHcmplcmpl0,2,1,1,2,2,1,2,1,
596NM_001048122chrX-1491087150857014910871508570101491087,1494593,1497021,1497931,1500252,1501918,1504135,1506221,1507206,1508547,1491446,1494715,1497184,1498066,1500389,1502342,1504258,1506343,1507356,1508570,0ARSLcmplcmpl1,2,1,1,2,1,1,2,2,0,
1235NM_001048121chr5-852041478520867985204147852086791385204147,85204580,85204768,85204924,85205518,85205872,85206231,85206870,85207087,85207433,85207654,85207867,85208556,85204299,85204650,85204834,85205030,85205748,85205998,85206334,85206935,85207163,85207558,85207782,85207976,85208679,0HSF4cmplcmpl1,0,0,2,0,0,2,0,2,0,1,0,0,
1100NM_001048120chr5+675312926755926867531292675592681467531292,67537563,67538175,67538694,67541513,67542701,67542848,67543276,67545307,67548817,67549833,67555188,67557070,67559181,67531409,67537687,67538250,67538797,67541657,67542768,67542976,67543416,67545411,67548954,67549936,67555310,67557188,67559268,0GALNScmplcmpl0,0,1,1,2,2,0,2,1,0,2,0,2,0,
755NM_001048119chr5-22333412223470212233341422347016922333412,22335160,22335473,22336237,22339534,22341168,22343623,22344500,22346949,22333713,22335382,22335684,22336398,22339704,22341278,22343668,22344667,22347021,0HTR3Acmplcmpl1,1,0,1,2,0,0,1,0,
1057NM_001048118chr4+61991530619969326199153061996932261991530,61995524,61991850,61996932,0ARSIcmplcmpl0,2,
89NM_001048117chr3-16875155169096751687515516909675816875155,16877855,16886192,16889362,16892332,16901163,16906119,16909537,16875430,16878080,16886417,16889534,16892615,16901323,16906249,16909675,0ARSKcmplcmpl1,1,1,0,2,1,0,0,

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