Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DsuzGB1 Primary Table: cds_mapping Row Count: 65,961 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | AWUT01012676 | varchar(255) | values |
| chromStart | 21768 | int(10) unsigned | range |
| chromEnd | 22095 | int(10) unsigned | range |
| name | Parp1:3_1001_2 | varchar(255) | values |
| score | 620 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 21768 | int(10) unsigned | range |
| thickEnd | 22095 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 6 | int(11) | range |
| blockSizes | 3,9,3,252,6,48, | longblob | |
| chromStarts | 0,3,15,18,270,279, | longblob | |
| id | Parp1:3_1001_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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| AWUT01012676 | 21768 | 22095 | Parp1:3_1001_2 | 620 | - | 21768 | 22095 | 0 | 6 | 3,9,3,252,6,48, | 0,3,15,18,270,279, | Parp1:3_1001_2 | E-value: 7.1e-58Reading frame: -3Bit score: 219Percent identity: ... |
| AWUT01012676 | 22151 | 22292 | Parp1:2_1001_0 | 746 | - | 22151 | 22292 | 0 | 1 | 141, | 0, | Parp1:2_1001_0 | E-value: 5.9e-27Reading frame: -1Bit score: 116Percent identity: ... |
| AWUT01012676 | 44639 | 44753 | Parp1:1_1001_0 | 580 | - | 44639 | 44753 | 0 | 1 | 114, | 0, | Parp1:1_1001_0 | E-value: 8.4e-18Reading frame: -1Bit score: 86Percent identity: 7 ... |
| AWUT01013263 | 71302 | 71440 | DIP-epsilon:1_12161_0 | 452 | + | 71302 | 71440 | 0 | 3 | 27,3,105, | 0,27,33, | DIP-epsilon:1_12161_0 | E-value: 3.1e-14Reading frame: +2Bit score: 74Percent identity: 7 ... |
| AWUT01013449 | 8278 | 8365 | IntS3:1_12755_0 | 450 | + | 8278 | 8365 | 0 | 1 | 87, | 0, | IntS3:1_12755_0 | E-value: 3.3e-09Reading frame: +2Bit score: 57Percent identity: 7 ... |
| AWUT01013449 | 8440 | 9049 | IntS3:2_12755_0 | 764 | + | 8440 | 9049 | 0 | 1 | 609, | 0, | IntS3:2_12755_0 | E-value: 4.9e-141Reading frame: +2Bit score: 495Percent identity: ... |
| AWUT01013449 | 56666 | 57299 | IntS3:3_12755_1 | 906 | + | 56666 | 57299 | 0 | 1 | 633, | 0, | IntS3:3_12755_1 | E-value: 1.1e-164Reading frame: +3Bit score: 574Percent identity: ... |
| AWUT01013449 | 57355 | 57538 | IntS3:4_12755_0 | 540 | + | 57355 | 57538 | 0 | 6 | 114,15,3,3,6,24, | 0,114,132,135,141,159, | IntS3:4_12755_0 | E-value: 1.8e-20Reading frame: +2Bit score: 95Percent identity: 6 ... |
| AWUT01013449 | 57608 | 57812 | IntS3:5_12755_2 | 324 | + | 57608 | 57812 | 0 | 4 | 30,15,3,138, | 0,36,60,66, | IntS3:5_12755_2 | E-value: 4.9e-19Reading frame: +3Bit score: 90Percent identity: 6 ... |
| AWUT01013449 | 57866 | 58676 | IntS3:6_12755_0 | 800 | + | 57866 | 58676 | 0 | 1 | 810, | 0, | IntS3:6_12755_0 | E-value: 1.0e-193Reading frame: +3Bit score: 670Percent 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. suzukii 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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