Schema for Ensembl Genes - Ensembl Genes |
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Database: oviAri3 Primary Table: ensGene Row Count: 29,118 Data last updated: 2021-05-25
Format description: A gene prediction with some additional info.
On download server: MariaDB table dump directory
| field | example | SQL type | info | description |
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| bin | 73 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | ENSOART00000019126.1 | varchar(255) | values | Name of gene (usually transcript_id from GTF) |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| strand | - | char(1) | values | + or - for strand |
| txStart | 23391 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 176938 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 23391 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 176938 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 6 | int(10) unsigned | range | Number of exons |
| exonStarts | 23391,169733,169989,171519,... | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 23440,169827,170101,171615,... | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | ENSOARG00000017577.1 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
| cdsStartStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
| cdsEndStat | incmpl | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
| exonFrames | 2,1,0,0,1,0, | 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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| 73 | ENSOART00000019126.1 | chr1 | - | 23391 | 176938 | 23391 | 176938 | 6 | 23391,169733,169989,171519,171617,176868, | 23440,169827,170101,171615,171685,176938, | 0 | ENSOARG00000017577.1 | incmpl | incmpl | 2,1,0,0,1,0, |
| 585 | ENSOART00000022247.1 | chr1 | + | 49750 | 49903 | 49750 | 49903 | 1 | 49750, | 49903, | 0 | ENSOARG00000020430.1 | incmpl | incmpl | 0, |
| 585 | ENSOART00000019136.1 | chr1 | + | 79925 | 87689 | 79925 | 87689 | 4 | 79925,86099,86780,87552, | 80001,86462,87062,87689, | 0 | ENSOARG00000017587.1 | cmpl | cmpl | 0,1,1,1, |
| 585 | ENSOART00000027409.1 | chr1 | + | 91111 | 96882 | 96882 | 96882 | 2 | 91111,94215, | 92128,96882, | 0 | ENSOARG00000025485.1 | none | none | -1,-1, |
| 585 | ENSOART00000019146.1 | chr1 | - | 105667 | 108573 | 105667 | 108573 | 5 | 105667,106075,107180,107662,108457, | 105982,106525,107308,107790,108573, | 0 | ENSOARG00000017595.1 | cmpl | incmpl | 0,0,1,2,0, |
| 586 | ENSOART00000019162.1 | chr1 | - | 131385 | 157208 | 132045 | 157208 | 9 | 131385,141099,143268,145612,147187,150298,151174,152582,156850, | 132305,141265,143411,145694,147418,150492,151314,152640,157208, | 0 | ENSOARG00000017608.1 | cmpl | cmpl | 1,0,1,0,0,1,2,1,0, |
| 586 | ENSOART00000019171.1 | chr1 | + | 186409 | 193575 | 186409 | 193575 | 5 | 186409,187537,189621,191093,193467, | 186533,187646,189712,191291,193575, | 0 | ENSOARG00000017620.1 | incmpl | incmpl | 0,1,2,0,0, |
| 586 | ENSOART00000019185.1 | chr1 | - | 198803 | 230341 | 198993 | 230341 | 14 | 198803,199394,200351,200451,200650,201013,203369,203941,204277,204368,204774,206151,206350,230097, | 199134,199451,200447,200498,200729,201207,203449,204014,204333,204414,204873,206223,206452,230341, | 0 | ENSOARG00000017628.1 | cmpl | cmpl | 0,0,0,1,0,1,2,1,2,1,1,1,1,0, |
| 586 | ENSOART00000019196.1 | chr1 | + | 215758 | 249151 | 215758 | 249151 | 6 | 215758,216245,235438,236448,236656,249031, | 216244,216930,235580,236573,236760,249151, | 0 | ENSOARG00000017642.1 | incmpl | cmpl | 0,0,1,2,1,0, |
| 73 | ENSOART00000019206.1 | chr1 | - | 258428 | 268599 | 258428 | 268599 | 5 | 258428,258866,259163,265660,268475, | 258554,258924,259242,265792,268599, | 0 | ENSOARG00000017652.1 | cmpl | incmpl | 0,2,1,1,0, |
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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 by Ensembl.
For more information on the different gene tracks, see our Genes FAQ.
Methods
For a description of the methods used in Ensembl gene predictions, please refer to
Hubbard et al. (2002), also listed in the References section below.
Data access
Ensembl Gene data can be explored interactively using the
Table Browser or the
Data Integrator.
For local downloads, the genePred format files for oviAri3 are available in our
downloads directory as ensGene.txt.gz or in our
genes download directory in GTF format.
For programmatic access, the data can be queried from the
REST API or
directly from our public MySQL
servers. Instructions on this method are available on our
MySQL help page and on
our blog.
Previous versions of this track can be found on our archive download server.
Credits
We would like to thank Ensembl for providing these gene annotations. For more information, please see
Ensembl's genome annotation page.
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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