Schema for mgcGenes
  Database: danRer5    Primary Table: mgcGenes    Row Count: 19,050   Data last updated: 2020-01-27
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 BC159105varchar(255) values Name of gene (usually transcript_id from GTF)
chrom Zv7_NA1varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 81565int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 88180int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 82493int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 87381int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 3int(10) unsigned range Number of exons
exonStarts 81565,82396,86560,longblob   Exon start positions (or end positions for minus strand item)
exonEnds 81789,82548,88180,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 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 -1,0,1,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
        danRer5.all_mrna.qName (via mgcGenes.name)
      danRer5.mgcFullMrna.qName (via mgcGenes.name)
      danRer5.mrnaOrientInfo.name (via mgcGenes.name)
      hgFixed.gbCdnaInfo.acc (via mgcGenes.name)
      hgFixed.gbSeq.acc (via mgcGenes.name)
      hgFixed.imageClone.acc (via mgcGenes.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585BC159105Zv7_NA1+81565881808249387381381565,82396,86560,81789,82548,88180,0cmplcmpl-1,0,1,
585BC096928Zv7_NA1+92861958229458495444392861,93613,94570,92912,93764,95822,0cmplcmpl-1,-1,0,
585BC076296Zv7_NA1-1103951214521103951213576110395,111060,112340,116511,118284,121327,110464,111185,112428,116642,118372,121452,0incmplcmpl0,1,0,1,0,0,
585BC055124Zv7_NA1000-16666339631666633759216666,33600,16835,33963,0incmplcmpl0,0,
585BC153528Zv7_NA1001-91575124901917771249011091575,94668,96489,99149,99400,104758,109317,110746,117536,124798,91821,94834,96601,99277,99470,104832,109358,110792,117635,124901,0cmplincmpl1,0,2,0,2,0,1,0,0,2,
585BC124534Zv7_NA1001-9419212490194525124901994192,96489,99149,99400,104758,109317,110746,117536,124798,94834,96601,99277,99470,104832,109358,110792,117635,124901,0cmplincmpl0,2,0,2,0,1,0,0,2,
585BC164803Zv7_NA1001-9452612490194526124901994526,96489,99149,99400,104758,109317,110746,117536,124798,94834,96601,99277,99470,104832,109358,110792,117635,124901,0incmplincmpl0,2,0,2,0,1,0,0,2,
585BC163168Zv7_NA1002+49076492274909749227149076,49227,0cmplincmpl0,
585BC163179Zv7_NA1002+49076492274909749227149076,49227,0cmplincmpl0,
585BC098551Zv7_NA1005+26021689525343968372826021,35286,53413,55949,60694,64788,68124,68784,26094,35375,53484,56040,60928,64887,68731,68952,0cmplcmpl-1,-1,0,0,1,1,1,-1,

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