Schema for wgEncodeGencodePseudoGeneVM35 |
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Database: mm39 Primary Table: wgEncodeGencodePseudoGeneVM35 Row Count: 13,774 Data last updated: 2024-05-14
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 | 610 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | ENSMUST00000192857.2 | 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 | 3322979 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3323459 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 3322979 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 3322979 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | range | Number of exons |
| exonStarts | 3322979, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3323459, | 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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| 610 | ENSMUST00000192857.2 | chr1 | + | 3322979 | 3323459 | 3322979 | 3322979 | 1 | 3322979, | 3323459, | 0 | Gm18956 | none | none | -1, |
| 612 | ENSMUST00000192183.2 | chr1 | + | 3602017 | 3602943 | 3602017 | 3602017 | 1 | 3602017, | 3602943, | 0 | Gm7341 | none | none | -1, |
| 618 | ENSMUST00000195384.2 | chr1 | - | 4326456 | 4330742 | 4326456 | 4326456 | 2 | 4326456,4329069, | 4326650,4330742, | 0 | Gm6101 | none | none | -1,-1, |
| 620 | ENSMUST00000195361.2 | chr1 | + | 4593127 | 4596960 | 4593127 | 4593127 | 2 | 4593127,4594668, | 4593826,4596960, | 0 | Gm7357 | none | none | -1,-1, |
| 620 | ENSMUST00000193889.2 | chr1 | - | 4605059 | 4605509 | 4605059 | 4605059 | 1 | 4605059, | 4605509, | 0 | Gm38076 | none | none | -1, |
| 620 | ENSMUST00000192738.2 | chr1 | + | 4680693 | 4681629 | 4680693 | 4680693 | 1 | 4680693, | 4681629, | 0 | Gm7369 | none | none | -1, |
| 621 | ENSMUST00000182774.2 | chr1 | - | 4758156 | 4759626 | 4758156 | 4758156 | 1 | 4758156, | 4759626, | 0 | Gm6085 | none | none | -1, |
| 621 | ENSMUST00000193443.2 | chr1 | - | 4762441 | 4763647 | 4762441 | 4762441 | 1 | 4762441, | 4763647, | 0 | Gm6119 | none | none | -1, |
| 621 | ENSMUST00000195671.2 | chr1 | - | 4805268 | 4805899 | 4805268 | 4805268 | 1 | 4805268, | 4805899, | 0 | Gm2053 | none | none | -1, |
| 621 | ENSMUST00000193658.2 | chr1 | + | 4841353 | 4842422 | 4841353 | 4841353 | 1 | 4841353, | 4842422, | 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