Schema for refGene
  Database: cavPor3    Primary Table: refGene    Row Count: 491   Data last updated: 2020-08-18
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 589smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001172907varchar(255) values Name of gene (usually transcript_id from GTF)
chrom scaffold_107varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 598462int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 610542int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 598511int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 610343int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 10int(10) unsigned range Number of exons
exonStarts 598462,598850,599170,599865...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 598554,599069,599265,599983...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Acrbpvarchar(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 0,1,1,0,1,2,0,0,0,0,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
        cavPor3.all_est.qName (via refGene.name)
      cavPor3.all_mrna.qName (via refGene.name)
      cavPor3.mrnaOrientInfo.name (via refGene.name)
      cavPor3.refFlat.name (via refGene.name)
      cavPor3.refSeqAli.qName (via refGene.name)
      cavPor3.xenoMrna.qName (via refGene.name)
      cavPor3.xenoRefGene.name (via refGene.name)
      cavPor3.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
589NM_001172907scaffold_107+59846261054259851161034310598462,598850,599170,599865,603156,604280,607650,607932,609657,610220,598554,599069,599265,599983,603625,604413,607830,608100,609741,610542,0Acrbpcmplcmpl0,1,1,0,1,2,0,0,0,0,
631NM_001172996scaffold_76-611835361203396118745612033436118353,6119220,6120188,6118822,6119261,6120339,0Pde6gcmplcmpl1,2,0,
675NM_001173098scaffold_2-118283311189594911828331118959492111828331,11829405,11830065,11832268,11832788,11833083,11833356,11833604,11836932,11838594,11841133,11842252,11844287,11844934,11 ...11828421,11829572,11830228,11832416,11832891,11833207,11833429,11833715,11837084,11838669,11841268,11842329,11844373,11845000,11 ...0Arntcmplcmpl0,1,0,2,1,0,2,2,0,0,0,1,2,2,1,0,2,2,0,1,0,
968NM_001172994scaffold_8+50252140502533195025218850253310150252140,50253319,0P2ry1cmplcmpl0,
98NM_001173109scaffold_22+265842352662192926584333266217211426584235,26586993,26588691,26591208,26598968,26601381,26602222,26605246,26608197,26609651,26609979,26620539,26621169,26621537,26584385,26587201,26588833,26591342,26599122,26601486,26602327,26605285,26608338,26609732,26610127,26620671,26621242,26621929,0Ces1dcmplcmpl0,1,2,0,2,0,0,0,0,0,0,1,1,2,
589NM_001173105scaffold_47-63172064702463174064702414631720,632376,633641,634510,635915,637251,638475,639893,641531,642533,643207,645157,646202,646945,631782,632509,633865,634649,636013,637384,638690,640023,641629,642666,643419,645290,646260,647024,0Albcmplcmpl0,2,0,2,0,2,0,2,0,2,0,2,1,0,
601NM_001173095scaffold_95+2118414212515421184142124075112118414,2119066,2119075,2121056,2121379,2121840,2122697,2123228,2123394,2123962,2124010,2118656,2119075,2119132,2121256,2121583,2121995,2122864,2123307,2123583,2124010,2125154,0Cyp11b2cmplcmpl0,2,0,2,1,1,0,2,0,0,1,
657NM_001172847scaffold_65+944821194499399448337944983049448211,9449059,9449458,9449668,9448451,9449206,9449584,9449939,0Fth1cmplcmpl0,0,0,0,
608NM_001172879scaffold_86+305153130533793051944305327363051531,3051932,3052146,3052717,3052982,3053214,3051607,3052002,3052484,3052849,3053100,3053379,0Mbp2cmplcmpl-1,0,1,0,0,1,
896NM_001172929scaffold_12+40808494408260124082208640825743440808494,40822079,40824673,40825665,40808515,40822186,40824858,40826012,0Cgacmplcmpl-1,0,1,0,

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