Schema for CDS Mapping - TBLASTN Mapping of D. melanogaster CDS |
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Database: DtakGB2 Primary Table: cds_mapping Row Count: 63,922 Data last updated: 2024-01-05
| field | example | SQL type | info |
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| chrom | AFFI02000003 | varchar(255) | values |
| chromStart | 10548 | int(10) unsigned | range |
| chromEnd | 11328 | int(10) unsigned | range |
| name | d4:6_4940_2 | varchar(255) | values |
| score | 746 | int(10) unsigned | range |
| strand | - | char(1) | values |
| thickStart | 10548 | int(10) unsigned | range |
| thickEnd | 11328 | int(10) unsigned | range |
| reserved | 0 | int(10) unsigned | range |
| blockCount | 7 | int(11) | range |
| blockSizes | 384,12,54,9,63,99,141, | longblob | |
| chromStarts | 0,387,405,462,471,537,639, | longblob | |
| id | d4:6_4940_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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| AFFI02000003 | 10548 | 11328 | d4:6_4940_2 | 746 | - | 10548 | 11328 | 0 | 7 | 384,12,54,9,63,99,141, | 0,387,405,462,471,537,639, | d4:6_4940_2 | E-value: 1.8e-164Reading frame: -2Bit score: 573Percent identity: ... |
| AFFI02000003 | 30913 | 31153 | d4:5_4940_0 | 800 | - | 30913 | 31153 | 0 | 1 | 240, | 0, | d4:5_4940_0 | E-value: 4.6e-50Reading frame: -1Bit score: 193Percent identity: ... |
| AFFI02000003 | 30913 | 31177 | d4:2_4940_2 | 820 | - | 30913 | 31177 | 0 | 1 | 264, | 0, | d4:2_4940_2 | E-value: 5.6e-56Reading frame: -1Bit score: 212Percent identity: ... |
| AFFI02000003 | 30916 | 31177 | d4:3_4940_2 | 818 | - | 30916 | 31177 | 0 | 1 | 261, | 0, | d4:3_4940_2 | E-value: 2.6e-55Reading frame: -1Bit score: 210Percent identity: ... |
| AFFI02000003 | 30919 | 31177 | d4:4_4940_2 | 814 | - | 30919 | 31177 | 0 | 1 | 258, | 0, | d4:4_4940_2 | E-value: 1.2e-54Reading frame: -1Bit score: 208Percent identity: ... |
| AFFI02000003 | 31970 | 32417 | d4:1_4940_0 | 754 | - | 31970 | 32417 | 0 | 3 | 36,3,405, | 0,39,42, | d4:1_4940_0 | E-value: 1.7e-98Reading frame: -3Bit score: 354Percent identity: ... |
| AFFI02000003 | 39357 | 39894 | CG3107:1_4938_0 | 616 | + | 39357 | 39894 | 0 | 8 | 21,6,6,3,15,18,12,438, | 0,24,36,42,48,69,87,99, | CG3107:1_4938_0 | E-value: 1.0e-98Reading frame: +1Bit score: 355Percent identity: ... |
| AFFI02000003 | 39951 | 42474 | CG3107:2_4938_1 | 508 | + | 39951 | 42474 | 0 | 7 | 1086,3,471,3,837,3,108, | 0,1089,1092,1563,1572,2412,2415, | CG3107:2_4938_1 | E-value: 0.Reading frame: +1Bit score: 1602Percent identity: 74.7 ... |
| AFFI02000009 | 10234 | 11044 | yellow-e:1_9880_0 | 934 | + | 10234 | 11044 | 0 | 1 | 810, | 0, | yellow-e:1_9880_0 | E-value: 4.9e-210Reading frame: +2Bit score: 724Percent identity: ... |
| AFFI02000009 | 11517 | 12294 | yellow-e:2_9880_1 | 900 | + | 11517 | 12294 | 0 | 1 | 777, | 0, | yellow-e:2_9880_1 | E-value: 6.0e-191Reading frame: +1Bit score: 661Percent 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. takahashii 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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