Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DgriCAF1 Primary Table: cds_mapping Row Count: 67,154 Data last updated: 2024-08-24
| field | example | SQL type | info |
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| chrom | scaffold_10012 | varchar(255) | values |
| chromStart | 66 | int(10) unsigned | range |
| chromEnd | 438 | int(10) unsigned | range |
| name | CG33643:1_11275_0 | varchar(255) | values |
| score | 0 | int(10) unsigned | range |
| strand | + | char(1) | values |
| thickStart | 66 | int(10) unsigned | range |
| thickEnd | 438 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 14 | int(11) | range |
| blockSizes | 9,3,6,78,6,81,3,12,6,3,18,8... | longblob | |
| chromStarts | 0,12,15,21,102,108,189,192,... | longblob | |
| id | CG33643:1_11275_0 | 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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| scaffold_10012 | 66 | 438 | CG33643:1_11275_0 | 0 | + | 66 | 438 | 0 | 14 | 9,3,6,78,6,81,3,12,6,3,18,84,15,12, | 0,12,15,21,102,108,189,192,216,222,225,249,333,360, | CG33643:1_11275_0 | E-value: 4.4e-05Reading frame: +1Bit score: 49Percent identity: 3 ... |
| scaffold_10012 | 114 | 438 | CG33641:1_11273_0 | 0 | + | 114 | 438 | 0 | 11 | 45,3,87,3,6,18,18,60,3,18,33, | 0,48,51,150,153,159,177,198,258,261,291, | CG33641:1_11273_0 | E-value: 2.0e-08Reading frame: +1Bit score: 60Percent identity: 3 ... |
| scaffold_10012 | 506 | 578 | CG33643:2_11275_0 | 418 | + | 506 | 578 | 0 | 1 | 72, | 0, | CG33643:2_11275_0 | E-value: 2.0e-05Reading frame: +3Bit score: 44Percent identity: 7 ... |
| scaffold_10012 | 506 | 593 | CG33642:2_11274_0 | 242 | + | 506 | 593 | 0 | 1 | 87, | 0, | CG33642:2_11274_0 | E-value: 5.6e-06Reading frame: +3Bit score: 46Percent identity: 6 ... |
| scaffold_10016 | 241 | 382 | alien:6_1315_1 | 958 | + | 241 | 382 | 0 | 1 | 141, | 0, | alien:6_1315_1 | E-value: 9.9e-31Reading frame: +2Bit score: 128Percent identity: ... |
| scaffold_10024 | 853 | 1033 | Cpr73D:4_7275_1 | 768 | + | 853 | 1033 | 0 | 1 | 180, | 0, | Cpr73D:4_7275_1 | E-value: 5.4e-37Reading frame: +2Bit score: 149Percent identity: ... |
| scaffold_10024 | 886 | 1033 | Cpr73D:3_7275_0 | 756 | + | 886 | 1033 | 0 | 1 | 147, | 0, | Cpr73D:3_7275_0 | E-value: 8.8e-29Reading frame: +2Bit score: 122Percent identity: ... |
| scaffold_10026 | 3148 | 3328 | Nrg:7_13329_2 | 590 | + | 3148 | 3328 | 0 | 7 | 12,3,12,12,15,54,9, | 0,15,21,51,69,96,171, | Nrg:7_13329_2 | E-value: 3.1e-07Reading frame: +2Bit score: 55Percent identity: 5 ... |
| scaffold_10027 | 233 | 419 | eIF4E3:2_13352_2 | 420 | + | 233 | 419 | 0 | 1 | 186, | 0, | eIF4E3:2_13352_2 | E-value: 3.9e-28Reading frame: +3Bit score: 119Percent identity: ... |
| scaffold_10027 | 486 | 558 | eIF4E3:3_13352_1 | 584 | + | 486 | 558 | 0 | 1 | 72, | 0, | eIF4E3:3_13352_1 | E-value: 1.1e-08Reading frame: +1Bit score: 55Percent identity: 7 ... |
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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. grimshawi 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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