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Schema for Genscan Genes - Genscan Gene Predictions |
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Database: bosTau4 Primary Table: genscan Row Count: 49,598
Format description: A gene prediction.
| field | example | SQL type | info | description |
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| bin | 585 | smallint unsigned | range | Indexing field to speed chromosome range queries. |
| name | chr1.1 | varchar(255) | values | Name of gene |
| chrom | chr1 | varchar(255) | values | Reference sequence chromosome or scaffold |
| strand | + | char(1) | values | + or - for strand |
| txStart | 27289 | int unsigned | range | Transcription start position |
| txEnd | 28224 | int unsigned | range | Transcription end position |
| cdsStart | 27289 | int unsigned | range | Coding region start |
| cdsEnd | 28224 | int unsigned | range | Coding region end |
| exonCount | 2 | int unsigned | range | Number of exons |
| exonStarts | 27289,28092, | longblob | | Exon start positions |
| exonEnds | 27574,28224, | longblob | | Exon end positions |
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| bin | name | chrom | strand | txStart | txEnd | cdsStart | cdsEnd | exonCount | exonStarts | exonEnds |
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| 585 | chr1.1 | chr1 | + | 27289 | 28224 | 27289 | 28224 | 2 | 27289,28092, | 27574,28224, |
| 585 | chr1.2 | chr1 | + | 37581 | 42175 | 37581 | 42175 | 4 | 37581,41212,41546,42039, | 37948,41493,41674,42175, |
| 585 | chr1.3 | chr1 | - | 61889 | 83053 | 61889 | 83053 | 2 | 61889,82665, | 62614,83053, |
| 73 | chr1.4 | chr1 | - | 103395 | 157695 | 103395 | 157695 | 9 | 103395,114362,115700,116377,117418,125967,133196,146007,156978, | 103557,114544,115807,116503,117528,126017,133313,146185,157695, |
| 586 | chr1.5 | chr1 | + | 219160 | 225412 | 219160 | 225412 | 3 | 219160,220418,225297, | 219406,220510,225412, |
| 586 | chr1.6 | chr1 | - | 241055 | 241571 | 241055 | 241571 | 1 | 241055, | 241571, |
| 587 | chr1.7 | chr1 | - | 271413 | 288105 | 271413 | 288105 | 3 | 271413,272298,288034, | 271633,272400,288105, |
| 587 | chr1.8 | chr1 | + | 327956 | 373071 | 327956 | 373071 | 6 | 327956,331232,333962,337305,352638,372975, | 328043,331406,334122,337453,352801,373071, |
| 587 | chr1.9 | chr1 | + | 383292 | 383682 | 383292 | 383682 | 1 | 383292, | 383682, |
| 588 | chr1.10 | chr1 | + | 398117 | 398450 | 398117 | 398450 | 1 | 398117, | 398450, |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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Genscan Genes (genscan) Track Description |
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Description
This track shows predictions from the
Genscan program
written by Chris Burge.
The predictions are based on transcriptional,
translational, and donor/acceptor splicing signals, as well as the length
and compositional distributions of exons, introns and intergenic regions.
Display Conventions and Configuration
This track follows the display conventions for
gene prediction
tracks.
The track description page offers the following filter and configuration
options:
- Color track by codons: Select the genomic codons option
to color and label each codon in a zoomed-in display to facilitate validation
and comparison of gene predictions. Click
here for more
information about this feature.
Methods
For a description of the Genscan program and the model that underlies it,
refer to Burge and Karlin (1997) in the References section below.
The splice site models used are described in more detail in Burge (1998)
below.
Credits
Thanks to Chris Burge for providing these data.
References
Burge C.
Modeling Dependencies in Pre-mRNA Splicing Signals.
In Salzberg S, Searls D, Kasif S, eds.
Computational Methods in Molecular Biology,
Elsevier Science, Amsterdam. 1998;127-163.
Burge C, Karlin S.
Prediction of Complete Gene Structures in Human Genomic DNA.
J. Mol. Biol. 1997 Apr 25;268(1):78-94.
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