Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DeugGB2 Primary Table: cds_mapping Row Count: 62,847 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | AFPQ02000020 | varchar(255) | values |
| chromStart | 9 | int(10) unsigned | range |
| chromEnd | 174 | int(10) unsigned | range |
| name | CG44098:6_13327_2 | varchar(255) | values |
| score | 1000 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 9 | int(10) unsigned | range |
| thickEnd | 174 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 1 | int(11) | range |
| blockSizes | 165, | longblob | |
| chromStarts | 0, | longblob | |
| id | CG44098:6_13327_2 | varchar(255) | values |
| description | | longblob | |
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Sample Rows
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| chrom | chromStart | chromEnd | name | score | strand | thickStart | thickEnd | reserved | blockCount | blockSizes | chromStarts | id | description |
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| AFPQ02000020 | 9 | 174 | CG44098:6_13327_2 | 1000 | + | 9 | 174 | 0 | 1 | 165, | 0, | CG44098:6_13327_2 | E-value: 1.6e-42Reading frame: +1Bit score: 166Percent identity: ... |
| AFPQ02000027 | 527 | 614 | sosie:5_9013_2 | 794 | - | 527 | 614 | 0 | 1 | 87, | 0, | sosie:5_9013_2 | E-value: 5.7e-14Reading frame: -3Bit score: 72Percent identity: 8 ... |
| AFPQ02000027 | 787 | 919 | sosie:4_9013_0 | 1000 | - | 787 | 919 | 0 | 1 | 132, | 0, | sosie:4_9013_0 | E-value: 6.1e-30Reading frame: -1Bit score: 125Percent identity: ... |
| AFPQ02000027 | 787 | 961 | sosie:3_9013_2 | 1000 | - | 787 | 961 | 0 | 1 | 174, | 0, | sosie:3_9013_2 | E-value: 1.9e-41Reading frame: -1Bit score: 163Percent identity: ... |
| AFPQ02000031 | 18381 | 18558 | Acox3:3_4205_0 | 492 | + | 18381 | 18558 | 0 | 1 | 177, | 0, | Acox3:3_4205_0 | E-value: 3.9e-29Reading frame: +1Bit score: 123Percent identity: ... |
| AFPQ02000031 | 18399 | 18558 | Acox3:2_4205_1 | 472 | + | 18399 | 18558 | 0 | 1 | 159, | 0, | Acox3:2_4205_1 | E-value: 1.4e-25Reading frame: +1Bit score: 111Percent identity: ... |
| AFPQ02000031 | 18699 | 18837 | Acox3:4_4205_0 | 734 | + | 18699 | 18837 | 0 | 2 | 54,81, | 0,57, | Acox3:4_4205_0 | E-value: 1.4e-27Reading frame: +1Bit score: 118Percent identity: ... |
| AFPQ02000031 | 18893 | 19382 | Acox3:5_4205_0 | 928 | + | 18893 | 19382 | 0 | 1 | 489, | 0, | Acox3:5_4205_0 | E-value: 2.4e-121Reading frame: +3Bit score: 429Percent identity: ... |
| AFPQ02000031 | 19440 | 19917 | Acox3:6_4205_1 | 888 | + | 19440 | 19917 | 0 | 1 | 477, | 0, | Acox3:6_4205_1 | E-value: 5.7e-113Reading frame: +1Bit score: 402Percent identity: ... |
| AFPQ02000031 | 21267 | 21531 | Acox3:7_4205_0 | 728 | + | 21267 | 21531 | 0 | 1 | 264, | 0, | Acox3:7_4205_0 | E-value: 8.4e-53Reading frame: +1Bit score: 202Percent identity: ... |
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Note: all start coordinates in our database are 0-based, not
1-based. See explanation
here.
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CDS Mapping (cds_mapping) Track Description
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Description
This track shows the tblastn alignment of the coding exons of D. melanogaster genes against
the D. eugracilis genome. The coding exon sequences were obtained from
FlyBase.
The tblastn search was performed using the following parameters:
-e=1e-2 -topComboN=1 -links -hspsepSmax=10000 -hspsepQmax=1000 -matrix=PAM40 -Q=7 -R=2
References
St Pierre SE, Ponting L, Stefancsik R, McQuilton P; FlyBase Consortium.
FlyBase 102 — advanced approaches to interrogating FlyBase.
Nucleic Acids Res. 2014 Jan;42(Database issue):D780-8
Gish, W. WU BLAST 2.0. (1996-2006)
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