Schema for refGene
  Database: xenTro7    Primary Table: refGene    Row Count: 8,995   Data last updated: 2020-09-02
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 642smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001005666varchar(255) values Name of gene (usually transcript_id from GTF)
chrom KB021651varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 7533880int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 7535207int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 7534446int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 7535118int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 1int(10) unsigned range Number of exons
exonStarts 7533880,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 7535207,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ppp1r3c.2varchar(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,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 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)
      xenTro7.all_est.qName (via refGene.name)
      xenTro7.all_mrna.qName (via refGene.name)
      xenTro7.mrnaOrientInfo.name (via refGene.name)
      xenTro7.refFlat.name (via refGene.name)
      xenTro7.refSeqAli.qName (via refGene.name)
      xenTro7.xenoRefGene.name (via refGene.name)
      xenTro7.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
642NM_001005666KB021651-753388075352077534446753511817533880,7535207,0ppp1r3c.2cmplcmpl0,
99NM_001005656KB021657+27475193275428442747559027540488427475193,27538345,27540076,27540351,27475672,27538573,27540351,27542844,0ubtd1cmplcmpl0,1,1,1,
1370NM_001005629KB021657-10301301110302132010301406710302117110103013011,103014229,103014501,103015240,103015881,103016250,103016473,103017185,103017418,103021141,103014151,103014351,103014652,103015356,103015969,103016393,103016537,103017341,103017520,103021320,0prmt1cmplcmpl0,1,0,1,0,1,0,0,0,0,
651NM_001005654KB021661-8740714876152587408008752233148740714,8742184,8742969,8743926,8744384,8745168,8747187,8747697,8748489,8750099,8751177,8751856,8752176,8761435,8740983,8742252,8743065,8744035,8744471,8745342,8747339,8747746,8748575,8750175,8751268,8751927,8752252,8761525,0orc4cmplcmpl0,1,1,0,0,0,1,0,1,0,2,0,0,-1,
864NM_001030414KB021656+36649669366521513664986636650589136649669,36652151,0cebpdcmplcmpl0,
101NM_001079150KB021650+300079283002273630010931300226711130007928,30010913,30011593,30012736,30015859,30016300,30016691,30017692,30019261,30020820,30022540,30007978,30011007,30011687,30012821,30015963,30016432,30016791,30017812,30019432,30020938,30022736,0ctnscmplcmpl-1,0,1,2,0,2,2,0,0,0,1,
622NM_001079111KB021651-4941658497570549424344966572174941658,4941840,4944794,4946742,4947780,4948927,4951212,4952422,4955067,4957788,4959194,4959523,4961403,4964138,4966099,4966449, ...4941806,4942599,4944992,4946855,4947889,4949096,4951307,4952573,4955261,4957944,4959381,4959648,4961486,4964346,4966279,4966597, ...0wdr91cmplcmpl-1,0,0,1,0,2,0,2,0,0,2,0,1,0,0,0,-1,
585NM_001079147KB022082-57595723276034572327457595,61136,62040,72135,60614,61260,62251,72327,0vgll4cmplincmpl1,0,2,2,
1026NM_001079146KB021649+579005735792490557900599579231461157900573,57905189,57907445,57908254,57913214,57914685,57914861,57917349,57918126,57920366,57923095,57900619,57905220,57907591,57908346,57913222,57914760,57914945,57917427,57918237,57920489,57924905,0pitpnb.2cmplcmpl0,2,0,2,1,0,0,0,0,0,0,
15NM_001278435KB021649+513293875139362451330784513922345351329387,51330748,51336498,51337537,51338568,51339520,51340791,51341316,51341666,51343523,51343659,51344566,51345473,51346498,51 ...51329446,51332101,51336562,51337624,51338879,51339802,51340977,51341457,51341745,51343561,51343755,51344624,51345652,51346676,51 ...0LOC100145162cmplcmpl-1,0,0,1,1,0,0,0,0,1,0,0,1,0,1,0,2,0,2,0,2,1,1,1,1,0,2,1,0,2,0,0,0,0,0,0,1,0,0,0,2,2,0,0,1,0,1,0,0,1,0,0,0,

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