Schema for orfeomeGenes
  Database: hg19    Primary Table: orfeomeGenes    Row Count: 35,184   Data last updated: 2019-02-21
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name KJ905121varchar(255) values Name of gene (usually transcript_id from GTF)
chrom chr1varchar(255) values Reference sequence chromosome or scaffold
strand -char(1) values + or - for strand
txStart 35139int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 35736int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 35736int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 35736int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 35139,35276,35720,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 35174,35481,35736,longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2  varchar(255) values Alternate name (e.g. gene_id from GTF)
cdsStartStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS start annotation (none, unknown, incomplete, or complete)
cdsEndStat unkenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames -1,-1,-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
        hg19.all_mrna.qName (via orfeomeGenes.name)
      hg19.mrnaOrientInfo.name (via orfeomeGenes.name)
      hg19.orfeomeMrna.qName (via orfeomeGenes.name)
      hgFixed.gbCdnaInfo.acc (via orfeomeGenes.name)
      hgFixed.gbSeq.acc (via orfeomeGenes.name)
      hgFixed.imageClone.acc (via orfeomeGenes.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585KJ905121chr1-35139357363573635736335139,35276,35720,35174,35481,35736,0unkunk-1,-1,-1,
587KJ899668chr1+3676583685953676583685951367658,368595,0cmplincmpl0,
589KJ899668chr1-6210976220346210976220341621097,622034,0incmplcmpl0,
590KJ901126chr1-7620817625727620817625711762081,762572,0incmplcmpl0,
591KJ905008chr1+8746878795328795328795328874687,876523,877515,877789,877938,878632,879077,879287,874840,876686,877631,877868,878438,878757,879188,879532,0unkunk-1,-1,-1,-1,-1,-1,-1,-1,
591KJ898602chr1-88007489462188007589462019880074,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,89 ...880180,880526,881033,881666,881925,883612,883983,886618,887519,887980,888668,889272,889462,891393,891595,892405,892653,894461,89 ...0incmplcmpl1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0,
591AM393843chr1-88007689462188007689462019880076,880436,880897,881552,881781,883510,883869,886506,887379,887791,888554,889161,889383,891302,891474,892273,892478,894308,89 ...880180,880526,881033,881666,881925,883612,883983,886618,887519,887980,888668,889272,889462,891393,891595,892405,892653,894461,89 ...0NOC2Lincmplcmpl1,1,0,0,0,0,0,2,0,0,0,0,2,1,0,0,2,2,0,
591BC166618chr1+89607390056989607390056912896073,896672,897008,897205,897734,898083,898488,898716,899299,899486,899728,900342,896180,896932,897130,897427,897851,898297,898633,898884,899388,899560,899910,900569,0KLHL17cmplincmpl0,2,1,0,0,0,1,2,2,1,0,2,
591KJ904192chr1+8970138976518970138976502897013,897205,897130,897651,0cmplincmpl0,0,
591AM393848chr1+90190990995290191190995216901909,902083,905656,905900,906065,906258,906492,906703,907454,907667,908240,908565,908879,909212,909695,909821,901994,902183,905803,905981,906138,906386,906588,906784,907530,907804,908390,908706,909020,909431,909744,909952,0PLEKHN1cmplincmpl0,2,0,0,0,1,0,0,0,1,0,0,0,0,0,1,

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