Schema for wgEncodeGencodeCompV43 |
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Database: hg38 Primary Table: wgEncodeGencodeCompV43 Row Count: 255,429 Data last updated: 2023-02-13
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 | 585 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | ENST00000456328.2 | 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 | 11868 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 14409 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 11868 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 11868 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 3 | int(10) unsigned | range | Number of exons |
| exonStarts | 11868,12612,13220, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 12227,12721,14409, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | DDX11L2 | varchar(255) | values | Alternate name (e.g. gene_id from GTF) |
| cdsStartStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS start annotation (none, unknown, incomplete, or complete) |
| cdsEndStat | none | enum('none', 'unk', 'incmpl', 'cmpl') | values | Status of CDS end annotation (none, unknown, incomplete, or complete) |
| exonFrames | -1,-1,-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. |
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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 | ENST00000456328.2 | chr1 | + | 11868 | 14409 | 11868 | 11868 | 3 | 11868,12612,13220, | 12227,12721,14409, | 0 | DDX11L2 | none | none | -1,-1,-1, |
| 585 | ENST00000619216.1 | chr1 | - | 17368 | 17436 | 17368 | 17368 | 1 | 17368, | 17436, | 0 | MIR6859-1 | none | none | -1, |
| 585 | ENST00000473358.1 | chr1 | + | 29553 | 31097 | 29553 | 29553 | 3 | 29553,30563,30975, | 30039,30667,31097, | 0 | MIR1302-2HG | none | none | -1,-1,-1, |
| 585 | ENST00000469289.1 | chr1 | + | 30266 | 31109 | 30266 | 30266 | 2 | 30266,30975, | 30667,31109, | 0 | MIR1302-2HG | none | none | -1,-1, |
| 585 | ENST00000607096.1 | chr1 | + | 30365 | 30503 | 30365 | 30365 | 1 | 30365, | 30503, | 0 | MIR1302-2 | none | none | -1, |
| 585 | ENST00000417324.1 | chr1 | - | 34553 | 36081 | 34553 | 34553 | 3 | 34553,35276,35720, | 35174,35481,36081, | 0 | FAM138A | none | none | -1,-1,-1, |
| 585 | ENST00000461467.1 | chr1 | - | 35244 | 36073 | 35244 | 35244 | 2 | 35244,35720, | 35481,36073, | 0 | FAM138A | none | none | -1,-1, |
| 585 | ENST00000642116.1 | chr1 | + | 57597 | 64116 | 57597 | 57597 | 3 | 57597,58699,62915, | 57653,58856,64116, | 0 | ENSG00000290826 | none | none | -1,-1,-1, |
| 585 | ENST00000641515.2 | chr1 | + | 65418 | 71585 | 65564 | 70008 | 3 | 65418,65519,69036, | 65433,65573,71585, | 0 | OR4F5 | cmpl | cmpl | -1,0,0, |
| 585 | ENST00000466430.5 | chr1 | - | 89294 | 120932 | 89294 | 89294 | 4 | 89294,92090,112699,120774, | 91629,92240,112804,120932, | 0 | ENSG00000238009 | none | none | -1,-1,-1,-1, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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US Server