Schema for Ensembl Genes - Ensembl Genes
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Database: fr3 Primary Table: ensGene Row Count: 29,241   Data last updated: 2019-01-14
Format description: A gene prediction with some additional info. On download server: MariaDB table dump directory
field | example | SQL type | info | description |
bin | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
name | ENSTRUT00000005856.2 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
chrom | HE591497 | varchar(255) | values | Reference sequence chromosome or scaffold |
strand | + | char(1) | values | + or - for strand |
txStart | 40405 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
txEnd | 50688 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
cdsStart | 40788 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
cdsEnd | 50688 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
exonCount | 8 | int(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 | 0 | int(11) | range | score |
name2 | ENSTRUG00000002511.2 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
cdsStartStat | cmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
cdsEndStat | cmpl | enum('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 | | 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. |
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Connected Tables and Joining Fields
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Sample Rows
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bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds | score | name2 | cdsStartStat | cdsEndStat | exonFrames |
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585 | ENSTRUT00000005856.2 | HE591497 | + | 40405 | 50688 | 40788 | 50688 | 8 | 40405,42043,42785,43051,43922,44088,46493,50615, | 40870,42243,42839,43125,44010,44217,46597,50688, | 0 | ENSTRUG00000002511.2 | cmpl | cmpl | 0,1,0,0,2,0,0,2, |
585 | ENSTRUT00000006231.2 | HE591497 | - | 53569 | 61770 | 53685 | 61425 | 13 | 53569,53767,54906,55082,55224,55859,56089,56361,56557,57625,58110,59426,61288, | 53688,53812,55002,55148,55315,56005,56231,56442,56645,57695,58182,59571,61770, | 0 | ENSTRUG00000002664.2 | cmpl | cmpl | 0,0,0,0,2,0,2,2,1,0,0,2,0, |
585 | ENSTRUT00000008003.2 | HE591497 | + | 73026 | 81943 | 73189 | 80858 | 12 | 73026,73747,74255,74577,75518,75814,76071,76504,76670,79960,80234,80549, | 73400,73908,74483,74748,75704,75926,76231,76593,76798,80164,80321,81943, | 0 | ENSTRUG00000003395.2 | cmpl | cmpl | 0,1,0,0,0,0,1,2,1,0,0,0, |
585 | ENSTRUT00000050040.1 | HE591497 | + | 82219 | 85969 | 82605 | 84526 | 6 | 82219,83347,83564,83756,83941,84376, | 82861,83498,83655,83852,84067,85969, | 0 | ENSTRUG00000019697.1 | cmpl | cmpl | 0,1,2,0,0,0, |
585 | ENSTRUT00000049383.1 | HE591497 | + | 85268 | 87429 | 85268 | 87429 | 4 | 85268,86772,87050,87339, | 85613,86880,87131,87429, | 0 | ENSTRUG00000022123.1 | cmpl | incmpl | 0,0,0,0, |
586 | ENSTRUT00000010510.2 | HE591497 | + | 156933 | 158771 | 156933 | 158771 | 3 | 156933,157259,158603, | 157182,157385,158771, | 0 | ENSTRUG00000004398.2 | incmpl | incmpl | 0,0,0, |
586 | ENSTRUT00000052881.1 | HE591497 | - | 161819 | 164145 | 161819 | 164145 | 4 | 161819,162402,162746,164122, | 161828,162583,162800,164145, | 0 | ENSTRUG00000023773.1 | cmpl | cmpl | 0,2,2,0, |
586 | ENSTRUT00000010704.2 | HE591497 | + | 162408 | 164989 | 162408 | 164989 | 4 | 162408,162573,164116,164835, | 162521,162794,164180,164989, | 0 | ENSTRUG00000004477.2 | cmpl | cmpl | 0,2,1,2, |
586 | ENSTRUT00000050108.1 | HE591497 | - | 172066 | 183597 | 174097 | 183451 | 2 | 172066,183364, | 174754,183597, | 0 | ENSTRUG00000024752.1 | cmpl | cmpl | 0,0, |
586 | ENSTRUT00000054445.1 | HE591497 | - | 198628 | 208717 | 198628 | 208717 | 6 | 198628,203597,203910,204834,206552,208597, | 199221,203870,203929,205136,206859,208717, | 0 | ENSTRUG00000023695.1 | cmpl | cmpl | 1,1,0,1,0,0, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Ensembl Genes (ensGene) Track Description
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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
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