Schema for wgEncodeGencodePseudoGeneVM24 |
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Database: mm10 Primary Table: wgEncodeGencodePseudoGeneVM24 Row Count: 14,602 Data last updated: 2020-01-16
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 | 609 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | ENSMUST00000192857.1 | 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 | 3252756 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3253236 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 3252756 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 3252756 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | range | Number of exons |
| exonStarts | 3252756, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3253236, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | Gm18956 | 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, | 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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| 609 | ENSMUST00000192857.1 | chr1 | + | 3252756 | 3253236 | 3252756 | 3252756 | 1 | 3252756, | 3253236, | 0 | Gm18956 | none | none | -1, |
| 611 | ENSMUST00000192183.1 | chr1 | + | 3531794 | 3532720 | 3531794 | 3531794 | 1 | 3531794, | 3532720, | 0 | Gm7341 | none | none | -1, |
| 617 | ENSMUST00000195384.1 | chr1 | - | 4256233 | 4260519 | 4256233 | 4256233 | 2 | 4256233,4258846, | 4256427,4260519, | 0 | Gm6101 | none | none | -1,-1, |
| 619 | ENSMUST00000195361.1 | chr1 | + | 4522904 | 4526737 | 4522904 | 4522904 | 2 | 4522904,4524445, | 4523603,4526737, | 0 | Gm7357 | none | none | -1,-1, |
| 619 | ENSMUST00000193889.1 | chr1 | - | 4534836 | 4535286 | 4534836 | 4534836 | 1 | 4534836, | 4535286, | 0 | Gm38076 | none | none | -1, |
| 620 | ENSMUST00000192738.1 | chr1 | + | 4610470 | 4611406 | 4610470 | 4610470 | 1 | 4610470, | 4611406, | 0 | Gm7369 | none | none | -1, |
| 620 | ENSMUST00000182774.1 | chr1 | - | 4687933 | 4689403 | 4687933 | 4687933 | 1 | 4687933, | 4689403, | 0 | Gm6085 | none | none | -1, |
| 620 | ENSMUST00000193443.1 | chr1 | - | 4692218 | 4693424 | 4692218 | 4692218 | 1 | 4692218, | 4693424, | 0 | Gm6119 | none | none | -1, |
| 621 | ENSMUST00000195671.1 | chr1 | - | 4735045 | 4735676 | 4735045 | 4735045 | 1 | 4735045, | 4735676, | 0 | Gm2053 | none | none | -1, |
| 621 | ENSMUST00000193658.1 | chr1 | + | 4771130 | 4772199 | 4771130 | 4771130 | 1 | 4771130, | 4772199, | 0 | Gm6123 | 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