Schema for refGene
  Database: papAnu4    Primary Table: refGene    Row Count: 509   Data last updated: 2019-05-22
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 824smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001293719varchar(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 31384217int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 31425790int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 31385344int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 31425443int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 12int(10) unsigned range Number of exons
exonStarts 31384217,31384492,31384724,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 31384399,31384613,31384937,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 AZIN2varchar(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,-1,0,0,0,2,2,0,1,0,2,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)
      papAnu4.all_est.qName (via refGene.name)
      papAnu4.all_mrna.qName (via refGene.name)
      papAnu4.mrnaOrientInfo.name (via refGene.name)
      papAnu4.refFlat.name (via refGene.name)
      papAnu4.refSeqAli.qName (via refGene.name)
      papAnu4.xenoRefGene.name (via refGene.name)
      papAnu4.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
824NM_001293719chr1+313842173142579031385344314254431231384217,31384492,31384724,31385272,31387056,31395155,31396449,31397706,31400298,31401652,31423156,31425304,31384399,31384613,31384937,31385449,31387230,31395328,31396584,31397872,31400461,31401765,31423371,31425790,0AZIN2cmplcmpl-1,-1,-1,0,0,0,2,2,0,1,0,2,
899NM_001173980chr1-41211164412432484121116441243248941211164,41211739,41213072,41213350,41213735,41214015,41214776,41215196,41243230,41211365,41211943,41213174,41213455,41213923,41214178,41215017,41215357,41243248,0SLC2A1cmplcmpl0,0,0,0,1,0,2,0,0,
1498NM_001112620chr12+1196926251197510281196926471197510065119692625,119745477,119746279,119746650,119750708,119693512,119745611,119746367,119746870,119751028,0UGT1A5Acmplcmpl0,1,0,1,2,
1511NM_001168943chr1-12144339612145359512144339612145359518121443396,121444875,121445301,121445520,121445695,121446058,121446488,121446906,121447346,121447759,121448611,121448874,12144920 ...121444430,121444971,121445346,121445576,121445773,121446205,121446662,121447059,121447478,121447977,121448700,121448994,12144929 ...0SEMA6Ccmplcmpl1,1,1,2,2,2,2,2,2,0,1,1,0,0,0,2,1,0,
1511NM_001168945chr1-1214722851214769821214722851214769823121472285,121473112,121476802,121472424,121473477,121476982,0LYSMD1cmplcmpl2,0,0,
1511NM_001168946chr1+1214778761214816631214778761214816637121477876,121478201,121478628,121478812,121479017,121480135,121481563,121477927,121478272,121478717,121478910,121479106,121480330,121481663,0SCNM1cmplcmpl0,0,2,1,0,2,2,
1511NM_001168947chr1-1214826651214866371214826651214866379121482665,121483103,121483503,121484015,121484215,121484805,121485712,121486152,121486514,121482688,121483248,121483647,121484123,121484346,121484895,121485829,121486309,121486637,0TMOD4cmplcmpl1,0,0,0,1,1,1,0,0,
188NM_001168948chr1-1214884301215062691214884301215062696121488430,121489618,121496594,121498738,121499030,121506152,121488818,121489763,121496771,121498853,121499183,121506269,0VPS72cmplcmpl2,1,1,0,0,0,
1512NM_001168949chr1+12151504612156327112151504612156327117121515046,121538937,121541605,121545395,121545974,121546277,121546349,121546359,121546384,121548493,121550949,121552620,12155387 ...121515131,121538969,121541686,121545526,121546092,121546348,121546359,121546384,121546421,121548795,121551155,121552704,12155392 ...0PIP5K1Acmplcmpl0,1,0,0,2,0,2,1,0,1,0,2,2,0,1,1,2,
1512NM_001168950chr1+12156897712158185112156897712158185110121568977,121576965,121578422,121579332,121579665,121579893,121580499,121580805,121581018,121581680,121569003,121577106,121578537,121579419,121579734,121580109,121580608,121580937,121581086,121581851,0PSMD4cmplcmpl0,2,2,0,0,0,0,1,1,0,

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