Schema for wgEncodeGencodeBasicVM31 |
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Database: mm39 Primary Table: wgEncodeGencodeBasicVM31 Row Count: 70,590 Data last updated: 2022-11-03
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 | ENSMUST00000193812.2 | 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 | 3143475 | int(10) unsigned | range | Transcription start position (or end position for minus strand item) |
| txEnd | 3144545 | int(10) unsigned | range | Transcription end position (or start position for minus strand item) |
| cdsStart | 3143475 | int(10) unsigned | range | Coding region start (or end position for minus strand item) |
| cdsEnd | 3143475 | int(10) unsigned | range | Coding region end (or start position for minus strand item) |
| exonCount | 1 | int(10) unsigned | range | Number of exons |
| exonStarts | 3143475, | longblob | | Exon start positions (or end positions for minus strand item) |
| exonEnds | 3144545, | 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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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 | ENSMUST00000193812.2 | chr1 | + | 3143475 | 3144545 | 3143475 | 3143475 | 1 | 3143475, | 3144545, | 0 | 4933401J01Rik | none | none | -1, |
| 609 | ENSMUST00000082908.3 | chr1 | + | 3172238 | 3172348 | 3172238 | 3172238 | 1 | 3172238, | 3172348, | 0 | Gm26206 | none | none | -1, |
| 76 | ENSMUST00000070533.5 | chr1 | - | 3284704 | 3741721 | 3286244 | 3741571 | 3 | 3284704,3491924,3740774, | 3287191,3492124,3741721, | 0 | Xkr4 | cmpl | cmpl | 1,2,0, |
| 611 | ENSMUST00000195335.2 | chr1 | - | 3435953 | 3438772 | 3435953 | 3435953 | 1 | 3435953, | 3438772, | 0 | Gm37180 | none | none | -1, |
| 611 | ENSMUST00000192336.2 | chr1 | - | 3445778 | 3448011 | 3445778 | 3445778 | 1 | 3445778, | 3448011, | 0 | Gm37363 | none | none | -1, |
| 611 | ENSMUST00000194099.2 | chr1 | - | 3535199 | 3537508 | 3535199 | 3535199 | 1 | 3535199, | 3537508, | 0 | Gm37686 | none | none | -1, |
| 76 | ENSMUST00000161581.2 | chr1 | + | 3536809 | 3583776 | 3536809 | 3536809 | 2 | 3536809,3583627, | 3536910,3583776, | 0 | Gm1992 | none | none | -1,-1, |
| 612 | ENSMUST00000192973.2 | chr1 | - | 3582673 | 3584730 | 3582673 | 3582673 | 1 | 3582673, | 3584730, | 0 | Gm37329 | none | none | -1, |
| 612 | ENSMUST00000195166.2 | chr1 | - | 3663114 | 3666126 | 3663114 | 3663114 | 1 | 3663114, | 3666126, | 0 | Gm38148 | none | none | -1, |
| 613 | ENSMUST00000192692.2 | chr1 | - | 3717531 | 3729127 | 3717531 | 3717531 | 2 | 3717531,3729069, | 3720732,3729127, | 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