Schema for refGene
  Database: oryLat2    Primary Table: refGene    Row Count: 903   Data last updated: 2020-08-19
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 689smallint(5) unsigned range Indexing field to speed chromosome range queries.
name NM_001104824varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr12varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 13634636int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 13644729int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 13634777int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 13642891int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 13int(10) unsigned range Number of exons
exonStarts 13634636,13635051,13635990,...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 13634834,13635174,13636049,...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 anxa4varchar(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 0,0,1,1,0,0,1,0,0,1,0,0,-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
        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)
      oryLat2.all_est.qName (via refGene.name)
      oryLat2.all_mrna.qName (via refGene.name)
      oryLat2.mrnaOrientInfo.name (via refGene.name)
      oryLat2.refFlat.name (via refGene.name)
      oryLat2.refSeqAli.qName (via refGene.name)
      oryLat2.xenoMrna.qName (via refGene.name)
      oryLat2.xenoRefGene.name (via refGene.name)
      oryLat2.xenoRefSeqAli.qName (via refGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
689NM_001104824chr12-136346361364472913634777136428911313634636,13635051,13635990,13638088,13638434,13638606,13640292,13640736,13641084,13641958,13642539,13642882,13644686,13634834,13635174,13636049,13638184,13638528,13638663,13640372,13640827,13641198,13642053,13642627,13642932,13644729,0anxa4cmplcmpl0,0,1,1,0,0,1,0,0,1,0,0,-1,
725NM_001122911chr10-18354969183621591835519318362159918354969,18356877,18357182,18358328,18358999,18359400,18359983,18360308,18361287,18355358,18357029,18357313,18358473,18359209,18359541,18360100,18360445,18362159,0ar-alphacmplcmpl0,1,2,1,1,1,1,2,0,
701NM_001128520chr23+15300175153011251530048615300957215300175,15300476,15300251,15301125,0ucn3lcmplcmpl-1,0,
827NM_001128519chr5-31842668318436343184293131843309231842668,31843579,31843321,31843634,0ucn2cmplcmpl0,-1,
701NM_001128518chr20+15300529153019561530111315301605215300529,15301093,15300599,15301956,0crhbcmplcmpl-1,0,
815NM_001128517chr5-30249289302608853024928930260885830249289,30250781,30252274,30254896,30255922,30257347,30258916,30260739,30249543,30250898,30252426,30255077,30256022,30257544,30259047,30260885,0vdrcmplcmpl1,1,2,1,0,1,2,0,
74NM_001128516chr7+156608915863261566089158632681566089,1567334,1576189,1577251,1580085,1582512,1582968,1586072,1566235,1567465,1576374,1577351,1580263,1582664,1583085,1586326,0vdralphacmplcmpl0,2,1,0,1,2,1,1,
619NM_001128513chr23-4498900457420644991314574206154498900,4506021,4506929,4507854,4509424,4509681,4516626,4517895,4527377,4530274,4530415,4531803,4534590,4536703,4574095,4499276,4506350,4506999,4507976,4509526,4509789,4516710,4517983,4527482,4530415,4530554,4531993,4534683,4536844,4574206,0foxp2cmplincmpl2,0,2,0,0,0,0,2,2,2,1,0,0,0,1,
761NM_001128512chr22+230725182315699123116822231549171123072518,23116601,23118439,23118711,23121041,23126646,23140030,23152777,23154716,23154862,23156365,23072621,23117118,23118627,23118828,23121410,23126785,23140164,23152961,23154862,23155049,23156991,0esr2bcmplcmpl-1,0,2,1,1,1,2,1,2,2,-1,
749NM_001128511chr6+21611405216123752161144021612297421611405,21611556,21611679,21611866,21611448,21611612,21611799,21612375,0LOC100169838cmplcmpl0,2,1,1,

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