Schema for refGene
  Database: equCab3    Primary Table: refGene    Row Count: 1,948   Data last updated: 2019-07-17
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 773smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001163859varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chrXvarchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 24727816int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 24732548int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 24727816int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 24732548int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 2int(10) unsigned range Number of exons
exonStarts 24727816,24731377,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 24728061,24732548,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 NR0B1varchar(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,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
        equCab3.all_est.qName (via refGene.name)
      equCab3.all_mrna.qName (via refGene.name)
      equCab3.mrnaOrientInfo.name (via refGene.name)
      equCab3.refFlat.name (via refGene.name)
      equCab3.refSeqAli.qName (via refGene.name)
      equCab3.xenoRefGene.name (via refGene.name)
      equCab3.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
773NM_001163859chrX-24727816247325482472781624732548224727816,24731377,24728061,24732548,0NR0B1cmplcmpl1,0,
823NM_001143797chr30-313073563131987031307538313197891131307356,31308326,31309778,31310205,31312806,31313662,31313985,31315396,31316044,31318450,31319764,31307783,31308453,31309892,31310391,31312930,31313787,31314151,31315453,31316246,31318480,31319870,0CHIT1cmplcmpl1,0,0,0,2,0,2,2,1,1,0,
117NM_001163828chr28-463783024643016846378302464301581246378302,46386301,46386778,46388095,46388674,46396069,46402606,46404902,46405682,46406348,46413631,46428791,46378486,46386456,46386888,46388223,46388810,46396174,46402867,46405215,46405811,46406480,46413788,46430168,0BRD1cmplcmpl2,0,1,2,1,1,1,0,0,0,2,0,
1056NM_001163824chr5-61776116617791176177611661777265261776116,61779037,61777429,61779117,0S1PR1cmplcmpl0,-1,
595NM_001163117chr31+1399599142885913996001426772211399599,1401200,1403189,1406305,1408471,1409375,1412025,1412465,1413461,1414196,1414403,1415033,1417565,1418457,1419989,1420748, ...1399652,1401757,1403274,1406502,1408612,1409472,1412196,1412642,1413635,1414324,1414556,1415252,1417673,1418617,1420108,1420983, ...0THBS2cmplcmpl0,1,0,1,0,0,1,1,1,1,0,0,0,0,1,0,1,1,0,2,1,
744NM_001308957chr1-209105622094397620911015209438972920910562,20911989,20912751,20913080,20913622,20913920,20914710,20915307,20916031,20917519,20919089,20921140,20922853,20923347,20 ...20911087,20912096,20912929,20913272,20913835,20914168,20914819,20915415,20916190,20917671,20919242,20921291,20922995,20923508,20 ...0SMC3cmplcmpl0,1,0,0,0,1,0,0,0,1,1,0,2,0,2,0,2,0,0,0,1,0,2,0,0,1,1,0,0,
734NM_001114177chr13-196021851962281819604360196227383219602185,19605012,19605400,19605643,19605963,19606158,19606375,19608373,19608547,19608717,19611057,19611408,19611570,19612402,19 ...19604459,19605123,19605502,19605757,19606047,19606266,19606454,19608457,19608627,19608834,19611199,19611482,19611702,19612557,19 ...0ITGAXcmplcmpl0,0,0,0,0,0,2,2,0,0,2,0,0,1,2,0,0,0,0,2,1,0,1,0,2,0,1,0,1,2,1,0,
1504NM_001082521chr1+1204822031204945341204822031204945349120482203,120485827,120487631,120488828,120489791,120492738,120493192,120493745,120494402,120482472,120485983,120487831,120489032,120489949,120492905,120493271,120493943,120494534,0CYP11A1cmplcmpl0,2,2,1,1,0,2,0,0,
1887NM_001308283chr1-17067065817075481217067184317075473935170670658,170672453,170674229,170679936,170681715,170683340,170685086,170686513,170688585,170690822,170693646,170695450,17069739 ...170672151,170672667,170674384,170680161,170681988,170683488,170685214,170686762,170688808,170691002,170693715,170695632,17069763 ...0HEATR5Acmplcmpl1,0,1,1,1,0,1,1,0,0,0,1,1,1,0,1,0,2,0,2,0,1,2,1,1,0,1,1,0,1,0,0,2,0,0,
853NM_001252304chr5-35200953352044853520151635204396635200953,35201813,35202305,35202808,35203722,35204335,35201685,35201907,35202584,35203087,35204019,35204485,0CD1E2cmplcmpl2,1,1,1,1,0,

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