Schema for wgEncodeGencodeBasicVM16 |
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Database: mm10 Primary Table: wgEncodeGencodeBasicVM16 Row Count: 64,505 Data last updated: 2017-12-17
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 | 608 | smallint(5) unsigned | range | Indexing field to speed chromosome range queries. |
| name | ENSMUST00000193812.1 | 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 | 3073252 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3074322 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 3073252 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 3073252 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | range | Number of exons |
| exonStarts | 3073252, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3074322, | longblob | | Exon end positions (or start positions for minus strand item) |
| score | 0 | int(11) | range | score |
| name2 | 4933401J01Rik | 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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To download this table in different text formats or to intersect or correlate it with other tables, use the Table Browser.
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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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| 608 | ENSMUST00000193812.1 | chr1 | + | 3073252 | 3074322 | 3073252 | 3073252 | 1 | 3073252, | 3074322, | 0 | 4933401J01Rik | none | none | -1, |
| 608 | ENSMUST00000082908.1 | chr1 | + | 3102015 | 3102125 | 3102015 | 3102015 | 1 | 3102015, | 3102125, | 0 | Gm26206 | none | none | -1, |
| 76 | ENSMUST00000070533.4 | chr1 | - | 3214481 | 3671498 | 3216021 | 3671348 | 3 | 3214481,3421701,3670551, | 3216968,3421901,3671498, | 0 | Xkr4 | cmpl | cmpl | 1,2,0, |
| 610 | ENSMUST00000195335.1 | chr1 | - | 3365730 | 3368549 | 3365730 | 3365730 | 1 | 3365730, | 3368549, | 0 | Gm37180 | none | none | -1, |
| 610 | ENSMUST00000192336.1 | chr1 | - | 3375555 | 3377788 | 3375555 | 3375555 | 1 | 3375555, | 3377788, | 0 | Gm37363 | none | none | -1, |
| 611 | ENSMUST00000194099.1 | chr1 | - | 3464976 | 3467285 | 3464976 | 3464976 | 1 | 3464976, | 3467285, | 0 | Gm37686 | none | none | -1, |
| 611 | ENSMUST00000161581.1 | chr1 | + | 3466586 | 3513553 | 3466586 | 3466586 | 2 | 3466586,3513404, | 3466687,3513553, | 0 | Gm1992 | none | none | -1,-1, |
| 611 | ENSMUST00000192973.1 | chr1 | - | 3512450 | 3514507 | 3512450 | 3512450 | 1 | 3512450, | 3514507, | 0 | Gm37329 | none | none | -1, |
| 612 | ENSMUST00000195166.1 | chr1 | - | 3592891 | 3595903 | 3592891 | 3592891 | 1 | 3592891, | 3595903, | 0 | Gm38148 | none | none | -1, |
| 612 | ENSMUST00000192692.1 | chr1 | - | 3647308 | 3658904 | 3647308 | 3647308 | 2 | 3647308,3658846, | 3650509,3658904, | 0 | Gm19938 | none | none | -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