Schema for mgcGenes
  Database: mm9    Primary Table: mgcGenes    Row Count: 27,556   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 618smallint(5) unsigned range Indexing field to speed chromosome range queries.
name BC120927varchar(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 4334455int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 4350349int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 4334680int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 4342906int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 4int(10) unsigned range Number of exons
exonStarts 4334455,4341990,4342282,435...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 4340172,4342162,4342918,435...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 1,0,0,-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 mgcGenes.name)
      hgFixed.gbSeq.acc (via mgcGenes.name)
      hgFixed.imageClone.acc (via mgcGenes.name)
      mm9.all_mrna.qName (via mgcGenes.name)
      mm9.mgcFullMrna.qName (via mgcGenes.name)
      mm9.mrnaOrientInfo.name (via mgcGenes.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
618BC120927chr1-433445543503494334680434290644334455,4341990,4342282,4350280,4340172,4342162,4342918,4350349,0cmplcmpl1,0,0,-1,
618BC120928chr1-433445543503494334680434290644334455,4341990,4342282,4350280,4340172,4342162,4342918,4350349,0cmplcmpl1,0,0,-1,
619BC148437chr1-448179844834894481799448348724481798,4483180,4482749,4483489,0incmplcmpl1,0,
619BC153021chr1-448179844834894481798448348724481798,4483180,4482749,4483489,0incmplcmpl1,0,
621BC021304chr1-476328947757914764532477575854763289,4767605,4772648,4774031,4775653,4764597,4767729,4772814,4774186,4775791,0cmplcmpl1,0,2,0,0,
621BC027233chr1-476328947757914764532477575854763289,4767605,4772648,4774031,4775653,4764597,4767729,4772814,4774186,4775791,0cmplcmpl1,0,2,0,0,
621BC052848chr1+479794248368154797994483509794797942,4798535,4818664,4820348,4822391,4827081,4829467,4831036,4835043,4798063,4798567,4818730,4820396,4822462,4827155,4829569,4831213,4836815,0cmplcmpl0,0,2,2,2,1,0,0,0,
621BC013536chr1+479797348368164797994483509794797973,4798535,4818664,4820348,4822391,4827081,4829467,4831036,4835043,4798063,4798567,4818730,4820396,4822462,4827155,4829569,4831213,4836816,0cmplcmpl0,0,2,2,2,1,0,0,0,
77BC061490chr1+4847894488798548479944886445104847894,4857550,4868107,4876824,4879537,4880820,4881995,4883497,4885014,4886436,4848057,4857613,4868213,4876912,4879683,4880877,4882150,4883644,4885086,4887985,0cmplcmpl0,0,0,1,2,1,1,0,0,0,
77BC006022chr1+4847899488755348479944886445104847899,4857550,4868107,4876824,4879537,4880820,4881995,4883497,4885014,4886436,4848057,4857613,4868213,4876912,4879683,4880877,4882150,4883644,4885086,4887553,0cmplcmpl0,0,0,1,2,1,1,0,0,0,

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