Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DbiaGB2 Primary Table: cds_mapping Row Count: 62,292 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | AFFD02000007 | varchar(255) | values |
| chromStart | 1257 | int(10) unsigned | range |
| chromEnd | 1659 | int(10) unsigned | range |
| name | kl-3:5_13655_2 | varchar(255) | values |
| score | 912 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 1257 | int(10) unsigned | range |
| thickEnd | 1659 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 1 | int(11) | range |
| blockSizes | 402, | longblob | |
| chromStarts | 0, | longblob | |
| id | kl-3:5_13655_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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| AFFD02000007 | 1257 | 1659 | kl-3:5_13655_2 | 912 | - | 1257 | 1659 | 0 | 1 | 402, | 0, | kl-3:5_13655_2 | E-value: 9.3e-103Reading frame: -3Bit score: 366Percent identity: ... |
| AFFD02000007 | 1717 | 1885 | kl-3:4_13655_0 | 750 | - | 1717 | 1885 | 0 | 1 | 168, | 0, | kl-3:4_13655_0 | E-value: 1.4e-35Reading frame: -2Bit score: 144Percent identity: ... |
| AFFD02000020 | 35 | 209 | CG8086:3_4331_0 | 898 | + | 35 | 209 | 0 | 1 | 174, | 0, | CG8086:3_4331_0 | E-value: 1.0e-38Reading frame: +3Bit score: 152Percent identity: ... |
| AFFD02000020 | 98 | 209 | CG8086:2_4331_0 | 946 | + | 98 | 209 | 0 | 1 | 111, | 0, | CG8086:2_4331_0 | E-value: 7.3e-24Reading frame: +3Bit score: 103Percent identity: ... |
| AFFD02000037 | 2935 | 2989 | Pcmt:1_11961_0 | 1000 | + | 2935 | 2989 | 0 | 1 | 54, | 0, | Pcmt:1_11961_0 | E-value: 4.0e-08Reading frame: +2Bit score: 53Percent identity: 1 ... |
| AFFD02000037 | 3053 | 3188 | Pcmt:2_11961_2 | 868 | + | 3053 | 3188 | 0 | 1 | 135, | 0, | Pcmt:2_11961_2 | E-value: 2.5e-27Reading frame: +3Bit score: 117Percent identity: ... |
| AFFD02000037 | 3441 | 3846 | Pcmt:3_11961_0 | 852 | + | 3441 | 3846 | 0 | 1 | 405, | 0, | Pcmt:3_11961_0 | E-value: 9.5e-93Reading frame: +1Bit score: 334Percent identity: ... |
| AFFD02000037 | 3441 | 3852 | Pcmt:4_11961_0 | 856 | + | 3441 | 3852 | 0 | 1 | 411, | 0, | Pcmt:4_11961_0 | E-value: 3.4e-94Reading frame: +1Bit score: 339Percent identity: ... |
| AFFD02000037 | 3906 | 3987 | Pcmt:5_11961_0 | 852 | + | 3906 | 3987 | 0 | 1 | 81, | 0, | Pcmt:5_11961_0 | E-value: 1.0e-14Reading frame: +1Bit score: 75Percent identity: 9 ... |
| AFFD02000037 | 5263 | 6022 | mia:1_1382_0 | 236 | + | 5263 | 6022 | 0 | 15 | 36,9,234,3,18,9,9,3,33,12,6,9,234,12,90, | 0,36,45,279,288,306,318,333,345,378,405,411,420,654,669, | mia:1_1382_0 | E-value: 9.9e-89Reading frame: +2Bit score: 321Percent 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. biarmipes 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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