Schema for refGene
  Database: criGriChoV2    Primary Table: refGene    Row Count: 589   Data last updated: 2019-05-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 1370smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001244039varchar(255) values Name of gene (usually transcript_id from GTF)
chrom LT883665v1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 102980836int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 102986494int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 102980913int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 102986215int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 102980836,102981936,1029823...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 102980916,102982151,1029825...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 Eef2varchar(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 0,0,2,1,0,2,0,2,0,0,0,0,1,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
        criGriChoV2.all_est.qName (via refGene.name)
      criGriChoV2.all_mrna.qName (via refGene.name)
      criGriChoV2.mrnaOrientInfo.name (via refGene.name)
      criGriChoV2.refFlat.name (via refGene.name)
      criGriChoV2.refSeqAli.qName (via refGene.name)
      criGriChoV2.xenoRefGene.name (via refGene.name)
      criGriChoV2.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
1370NM_001244039LT883665v1+10298083610298649410298091310298621513102980836,102981936,102982324,102982905,102983315,102983589,102983802,102984345,102984739,102984948,102985405,102985678,10298602 ...102980916,102982151,102982506,102983117,102983494,102983695,102984251,102984604,102984847,102985302,102985588,102985811,10298649 ...0Eef2cmplcmpl0,0,2,1,0,2,0,2,0,0,0,0,1,
710NR_105240LT883675v1+16451711164517861645178616451786116451711,16451786,0Mir450aunkunk-1,
1216NM_001244037LT883668v1-82789842827950658279036682795050782789842,82790578,82790844,82791058,82791525,82791770,82794947,82790492,82790689,82790963,82791144,82791658,82791836,82795065,0Mpdu1cmplcmpl0,0,1,2,1,1,0,
75NM_001243993LT883719v1+210098822393832100988223938372100988,2101266,2236799,2238467,2238869,2239155,2239339,2101061,2101536,2237075,2238743,2238983,2239192,2239383,0LOC100689008cmplincmpl0,1,1,1,1,1,2,
855NM_001244538LT883680v1+35489755354924933548975535492493335489755,35490245,35492427,35489863,35490320,35492493,0Dph3cmplcmpl0,0,0,
791NM_001244538LT883684v1+27110077271103262711007727110326127110077,27110326,0Dph3cmplcmpl0,
1663NM_001244045LT883664v1+14139481614141973214139483414141936913141394816,141400040,141402408,141403025,141407285,141408239,141409840,141410931,141411140,141412925,141414276,141418180,14141928 ...141394987,141400244,141402453,141403105,141407457,141408286,141409931,141411001,141411288,141413016,141414366,141418357,14141973 ...0Adslcmplcmpl0,0,0,0,2,0,2,0,1,2,0,0,0,
585NR_105252LT883834v1+76020760977609776097176020,76097,0Mir532unkunk-1,
602NM_001246806LT883697v1-233547823389822335478233561722335478,2338931,2335625,2338982,0S100bincmplcmpl0,-1,
1930NM_001246796LT883664v1+1763056881763225351763057181763223998176305688,176310695,176313207,176313426,176314995,176316898,176320346,176322263,176306023,176310804,176313346,176313477,176315060,176317040,176320845,176322535,0Casp8cmplcmpl0,2,0,1,1,0,1,2,

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