Schema for mgcGenes
  Database: danRer7    Primary Table: mgcGenes    Row Count: 18,264   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 BC157389varchar(255) values Name of gene (usually transcript_id from GTF)
chrom Zv9_NA110varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 3369int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 25536int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 3426int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 25536int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 15int(10) unsigned range Number of exons
exonStarts 3369,4371,5127,7177,8049,11...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 3564,4476,5209,7306,8102,11...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 incmplenum('none', 'unk', 'incmpl', 'cmpl') values Status of CDS end annotation (none, unknown, incomplete, or complete)
exonFrames 0,0,0,1,1,0,2,2,0,2,1,1,2,0,2,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
        danRer7.all_mrna.qName (via mgcGenes.name)
      danRer7.mgcFullMrna.qName (via mgcGenes.name)
      danRer7.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
585BC157389Zv9_NA110+336925536342625536153369,4371,5127,7177,8049,11127,13688,13992,14258,15888,16240,19924,20951,22766,25415,3564,4476,5209,7306,8102,11318,13754,14047,14338,16022,16315,20096,21168,22831,25536,0cmplincmpl0,0,0,1,1,0,2,2,0,2,1,1,2,0,2,
585BC048878Zv9_NA119-116138831161388341161,1983,3095,3815,1712,2099,3224,3883,0incmplincmpl2,0,0,1,
585BC165814Zv9_NA122-01293801293730,6871,12901,56,6998,12938,0incmplcmpl1,0,0,
585BC045451Zv9_NA122-01319601293730,6871,12901,56,6998,13196,0incmplcmpl1,0,0,
585BC065661Zv9_NA122-01320101293730,6871,12901,56,6998,13201,0incmplcmpl1,0,0,
585BC142829Zv9_NA123-39150449203944744906339150,41107,44692,40274,41251,44920,0cmplcmpl1,1,0,
585BC100007Zv9_NA15+18564217572167621757218564,21675,18677,21757,0cmplincmpl-1,0,
585BC154641Zv9_NA154-29657320563003832030129657,32056,0cmplcmpl0,
585BC171687Zv9_NA154-29809320543003832030129809,32054,0cmplcmpl0,
585BC171691Zv9_NA154-29809320543003832030129809,32054,0cmplcmpl0,

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