Schema for refGene
  Database: felCat5    Primary Table: refGene    Row Count: 449   Data last updated: 2020-08-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1300smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001278838varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrC1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 93829940int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 93843799int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 93829995int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 93843781int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 11int(10) unsigned range Number of exons
exonStarts 93829940,93831464,93836959,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 93830516,93831600,93837076,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 OVGP1varchar(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 1,0,0,0,2,0,2,2,1,1,0,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
        felCat5.all_est.qName (via refGene.name)
      felCat5.all_mrna.qName (via refGene.name)
      felCat5.mrnaOrientInfo.name (via refGene.name)
      felCat5.refFlat.name (via refGene.name)
      felCat5.refSeqAli.qName (via refGene.name)
      felCat5.xenoMrna.qName (via refGene.name)
      felCat5.xenoRefGene.name (via refGene.name)
      felCat5.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
1300NM_001278838chrC1-938299409384379993829995938437811193829940,93831464,93836959,93838633,93838915,93840296,93840902,93841291,93842502,93843120,93843756,93830516,93831600,93837076,93838819,93839024,93840421,93841068,93841348,93842707,93843150,93843799,0OVGP1cmplcmpl1,0,0,0,2,0,2,2,1,1,0,
856NM_001278835chrB3+355779013560477335577901356047731435577901,35594069,35595057,35596770,35597519,35598514,35599307,35600067,35601249,35601604,35602438,35602813,35603531,35604709,35578154,35594162,35595123,35596817,35597630,35598616,35599440,35600248,35601336,35601677,35602622,35602904,35603636,35604773,0HEXAcmplcmpl0,1,1,1,0,0,0,1,2,2,0,1,2,2,
1NM_001278832chrB2-8119598878072381205248760790168119598,8153433,8156697,8243120,8284678,8345287,8379169,8473379,8550983,8584529,8601020,8668100,8759202,8760620,8779781,8780612,8120710,8153598,8156781,8243183,8284859,8345433,8379336,8473483,8551104,8584578,8601117,8668185,8759315,8760795,8779825,8780723,0CDKAL1cmplcmpl0,0,0,0,2,0,1,2,1,0,2,1,2,0,-1,-1,
1064NM_001009205chrF1+62824857628310326282485762831032562824857,62825591,62825979,62829815,62830853,62824897,62825612,62826237,62830070,62831032,0FCGR3Acmplcmpl0,1,1,1,1,
773NM_001009190chrA3-24671749246761432467174924676143324671749,24674262,24675983,24671935,24674324,24676143,0ASIPcmplcmpl0,1,0,
1477NM_001009217chrA3+11700576711704630011700577311704630020117005767,117012158,117014037,117015550,117016905,117018433,117026628,117032164,117032751,117033842,117034752,117035304,11703651 ...117005815,117012216,117014134,117015660,117016989,117018603,117026752,117032284,117032848,117033967,117034886,117035392,11703659 ...0XDHcmplincmpl0,0,1,2,0,0,2,0,0,1,0,2,0,0,0,2,0,0,0,0,
181NM_001009377chrX+1134952461135265901134952461135265908113495246,113501608,113501973,113506593,113513431,113516114,113525271,113526042,113495334,113501772,113501998,113506707,113513560,113516332,113525386,113526590,0F9cmplcmpl0,1,0,1,1,1,0,1,
1141NM_001009375chrD2+73004381730049637300438173004963173004381,73004963,0ADRB1incmplincmpl2,
1369NM_001009374chrC1-1028798191028833171028812941028832274102879819,102881937,102882539,102883281,102881411,102882185,102883268,102883317,0MCL1cmplcmpl0,1,0,-1,
913NM_001009372chrD4-430010644303869543001064430386951543001064,43001939,43003716,43004047,43004359,43005040,43007775,43008729,43013762,43014751,43021106,43022046,43024633,43035478,43 ...43001125,43002051,43003929,43004150,43004430,43005096,43007894,43008958,43013838,43014848,43021169,43022151,43024772,43035555,43 ...0PSIP1cmplcmpl2,1,1,0,1,2,0,2,1,0,0,0,2,0,0,

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