Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DkikGB2 Primary Table: cds_mapping Row Count: 63,233 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | AFFH02000026 | varchar(255) | values |
| chromStart | 612 | int(10) unsigned | range |
| chromEnd | 969 | int(10) unsigned | range |
| name | kl-2:4_309_2 | varchar(255) | values |
| score | 624 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 612 | int(10) unsigned | range |
| thickEnd | 969 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 2 | int(11) | range |
| blockSizes | 42,297, | longblob | |
| chromStarts | 0,60, | longblob | |
| id | kl-2:4_309_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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| AFFH02000026 | 612 | 969 | kl-2:4_309_2 | 624 | - | 612 | 969 | 0 | 2 | 42,297, | 0,60, | kl-2:4_309_2 | E-value: 2.0e-64Reading frame: -1Bit score: 239Percent identity: ... |
| AFFH02000026 | 1031 | 1679 | kl-2:3_309_0 | 640 | - | 1031 | 1679 | 0 | 1 | 648, | 0, | kl-2:3_309_0 | E-value: 7.1e-141Reading frame: -2Bit score: 479Percent identity: ... |
| AFFH02000026 | 1677 | 1698 | kl-2:3_309_0 | 716 | - | 1677 | 1698 | 0 | 1 | 21, | 0, | kl-2:3_309_0 | E-value: 7.1e-141Reading frame: -1Bit score: 21Percent identity: ... |
| AFFH02000063 | 1231 | 1399 | Pkd2:1_9831_0 | 148 | - | 1231 | 1399 | 0 | 14 | 12,9,9,3,12,6,12,15,6,3,21,9,9,24, | 0,12,21,30,36,48,54,75,90,96,99,120,132,144, | Pkd2:1_9831_0 | E-value: 0.0020Reading frame: -2Bit score: 45Percent identity: 42 ... |
| AFFH02000283 | 1187 | 1367 | CG43123:2_12848_2 | 546 | - | 1187 | 1367 | 0 | 9 | 30,3,3,12,15,12,21,12,15, | 0,33,69,72,84,108,132,153,165, | CG43123:2_12848_2 | E-value: 3.3e-05Reading frame: -1Bit score: 51Percent identity: 4 ... |
| AFFH02000283 | 1236 | 1467 | Tango10:1_3228_0 | 478 | + | 1236 | 1467 | 0 | 11 | 24,12,15,15,36,51,18,12,9,12,6, | 0,27,39,54,72,108,165,183,198,210,225, | Tango10:1_3228_0 | E-value: 1.6e-16Reading frame: +1Bit score: 84Percent identity: 6 ... |
| AFFH02000283 | 1271 | 1466 | CG15040:3_3633_0 | 204 | - | 1271 | 1466 | 0 | 14 | 9,9,15,27,6,3,9,15,18,33,9,18,3,9, | 0,9,18,33,60,66,69,78,99,120,153,165,183,186, | CG15040:3_3633_0 | E-value: 6.4e-11Reading frame: -1Bit score: 67Percent identity: 4 ... |
| AFFH02000283 | 1314 | 1410 | CG42494:3_12266_2 | 334 | - | 1314 | 1410 | 0 | 7 | 15,15,15,15,3,18,15, | 0,15,30,45,60,63,81, | CG42494:3_12266_2 | E-value: 1.9e-05Reading frame: -3Bit score: 50Percent identity: 6 ... |
| AFFH02000335 | 35166 | 35340 | CG4783:2_8692_1 | 174 | - | 35166 | 35340 | 0 | 3 | 48,12,114, | 0,48,60, | CG4783:2_8692_1 | E-value: 5.7e-21Reading frame: -3Bit score: 96Percent identity: 6 ... |
| AFFH02000335 | 35166 | 35340 | CG4783:3_8692_1 | 174 | - | 35166 | 35340 | 0 | 3 | 48,12,114, | 0,48,60, | CG4783:3_8692_1 | E-value: 5.7e-21Reading frame: -3Bit score: 96Percent identity: 6 ... |
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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. kikkawai 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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