Schema for wgEncodeGencodePseudoGeneV43lift37 |
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Database: hg19 Primary Table: wgEncodeGencodePseudoGeneV43lift37 Row Count: 16,924 Data last updated: 2023-02-15
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 | ENST00000450305.2_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 | 12009 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 13670 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 12009 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 12009 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 6 | int(10) unsigned | range | Number of exons |
| exonStarts | 12009,12178,12612,12974,132... | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 12057,12227,12697,13052,133... | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | DDX11L1 | 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,-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 | ENST00000450305.2_2 | chr1 | + | 12009 | 13670 | 12009 | 12009 | 6 | 12009,12178,12612,12974,13220,13452, | 12057,12227,12697,13052,13374,13670, | 0 | DDX11L1 | none | none | -1,-1,-1,-1,-1,-1, |
| 585 | ENST00000488147.1_4 | chr1 | - | 14403 | 29570 | 14403 | 14403 | 11 | 14403,15004,15795,16606,16857,17232,17605,17914,18267,24737,29533, | 14501,15038,15947,16765,17055,17368,17742,18061,18366,24891,29570, | 0 | WASH7P | none | none | -1,-1,-1,-1,-1,-1,-1,-1,-1,-1,-1, |
| 585 | ENST00000606857.1_2 | chr1 | + | 52472 | 53312 | 52472 | 52472 | 1 | 52472, | 53312, | 0 | OR4G4P | none | none | -1, |
| 585 | ENST00000492842.2_3 | chr1 | + | 62948 | 63887 | 62948 | 62948 | 1 | 62948, | 63887, | 0 | OR4G11P | none | none | -1, |
| 73 | ENST00000442987.3_2 | chr1 | + | 131024 | 134836 | 131024 | 131024 | 1 | 131024, | 134836, | 0 | CICP27 | none | none | -1, |
| 586 | ENST00000494149.2_3 | chr1 | - | 135140 | 135895 | 135140 | 135140 | 1 | 135140, | 135895, | 0 | ENSG00000268903 | none | none | -1, |
| 586 | ENST00000595919.1_2 | chr1 | - | 137681 | 137965 | 137681 | 137681 | 1 | 137681, | 137965, | 0 | ENSG00000269981 | none | none | -1, |
| 587 | ENST00000514436.1 | chr1 | + | 326095 | 328112 | 326095 | 326095 | 2 | 326095,327347, | 326569,328112, | 0 | RP4-669L17.8 | none | none | -1,-1, |
| 587 | ENST00000432723.3 | chr1 | - | 329430 | 332236 | 329430 | 329430 | 2 | 329430,329949, | 329620,332236, | 0 | CICP7 | none | none | -1,-1, |
| 587 | ENST00000445840.1 | chr1 | + | 334125 | 334305 | 334125 | 334125 | 1 | 334125, | 334305, | 0 | RP4-669L17.4 | none | none | -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