Schema for Ensembl Genes - Ensembl Genes
  Database: fr3    Primary Table: ensGene    Row Count: 29,241   Data last updated: 2019-01-14
Format description: A gene prediction with some additional info.
fieldexampleSQL type info description
bin 585smallint(5) unsigned range Indexing field to speed chromosome range queries.
name ENSTRUT00000005856.2varchar(255) values Name of gene (usually transcript_id from GTF)
chrom HE591497varchar(255) values Reference sequence chromosome or scaffold
strand +char(1) values + or - for strand
txStart 40405int(10) unsigned range Transcription start position (or end position for minus strand item)
txEnd 50688int(10) unsigned range Transcription end position (or start position for minus strand item)
cdsStart 40788int(10) unsigned range Coding region start (or end position for minus strand item)
cdsEnd 50688int(10) unsigned range Coding region end (or start position for minus strand item)
exonCount 8int(10) unsigned range Number of exons
exonStarts 40405,42043,42785,43051,439...longblob   Exon start positions (or end positions for minus strand item)
exonEnds 40870,42243,42839,43125,440...longblob   Exon end positions (or start positions for minus strand item)
score 0int(11) range score
name2 ENSTRUG00000002511.2varchar(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 0,1,0,0,2,0,0,2,longblob   Exon frame {0,1,2}, or -1 if no frame for exon

Connected Tables and Joining Fields
        fr3.ensGtp.transcript (via ensGene.name)
      fr3.ensPep.name (via ensGene.name)
      fr3.ensemblSource.name (via ensGene.name)
      fr3.ensemblToGeneName.name (via ensGene.name)

Sample Rows
 
binnamechromstrandtxStarttxEndcdsStartcdsEndexonCountexonStartsexonEndsscorename2cdsStartStatcdsEndStatexonFrames
585ENSTRUT00000005856.2HE591497+40405506884078850688840405,42043,42785,43051,43922,44088,46493,50615,40870,42243,42839,43125,44010,44217,46597,50688,0ENSTRUG00000002511.2cmplcmpl0,1,0,0,2,0,0,2,
585ENSTRUT00000006231.2HE591497-535696177053685614251353569,53767,54906,55082,55224,55859,56089,56361,56557,57625,58110,59426,61288,53688,53812,55002,55148,55315,56005,56231,56442,56645,57695,58182,59571,61770,0ENSTRUG00000002664.2cmplcmpl0,0,0,0,2,0,2,2,1,0,0,2,0,
585ENSTRUT00000008003.2HE591497+730268194373189808581273026,73747,74255,74577,75518,75814,76071,76504,76670,79960,80234,80549,73400,73908,74483,74748,75704,75926,76231,76593,76798,80164,80321,81943,0ENSTRUG00000003395.2cmplcmpl0,1,0,0,0,0,1,2,1,0,0,0,
585ENSTRUT00000050040.1HE591497+82219859698260584526682219,83347,83564,83756,83941,84376,82861,83498,83655,83852,84067,85969,0ENSTRUG00000019697.1cmplcmpl0,1,2,0,0,0,
585ENSTRUT00000049383.1HE591497+85268874298526887429485268,86772,87050,87339,85613,86880,87131,87429,0ENSTRUG00000022123.1cmplincmpl0,0,0,0,
586ENSTRUT00000010510.2HE591497+1569331587711569331587713156933,157259,158603,157182,157385,158771,0ENSTRUG00000004398.2incmplincmpl0,0,0,
586ENSTRUT00000052881.1HE591497-1618191641451618191641454161819,162402,162746,164122,161828,162583,162800,164145,0ENSTRUG00000023773.1cmplcmpl0,2,2,0,
586ENSTRUT00000010704.2HE591497+1624081649891624081649894162408,162573,164116,164835,162521,162794,164180,164989,0ENSTRUG00000004477.2cmplcmpl0,2,1,2,
586ENSTRUT00000050108.1HE591497-1720661835971740971834512172066,183364,174754,183597,0ENSTRUG00000024752.1cmplcmpl0,0,
586ENSTRUT00000054445.1HE591497-1986282087171986282087176198628,203597,203910,204834,206552,208597,199221,203870,203929,205136,206859,208717,0ENSTRUG00000023695.1cmplcmpl1,1,0,1,0,0,

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

Ensembl Genes (ensGene) Track Description
 

Description

These gene predictions were generated using the Ensembl annotation system.

Methods

For a description of the methods used in Ensembl gene prediction, refer to Hubbard et al. (2002) in the References section below.

Credits

The Fugu genome was annotated using the Ensembl system by the Fugu informatics group at the Institute of Molecular and Cell Biology (IMCB) in Singapore. Thanks to IMCB's Shawn Hoon for providing these annotations.

References

Hubbard T, Barker D, Birney E, Cameron G, Chen Y, Clark L, Cox T, Cuff J, Curwen V, Down T et al. The Ensembl genome database project. Nucleic Acids Res. 2002 Jan 1;30(1):38-41. PMID: 11752248; PMC: PMC99161