ubiD:Gene
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| Quickview | Gene | Gene Product(s) | Expression | Evolution | On One Page |
| Nomenclature | Location(s) and DNA Sequence | Sequence Features | Alleles and Phenotypes | Genetic Interactions | Genetic Resources | Accessions | Links | References | Suggestions |
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Nomenclature
See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.
| Standard name |
ubiD |
|---|---|
| Mnemonic |
Ubiquinone |
| Synonyms |
ECK3835, b3843, JW3819, yigC, yigY[1], yigY |
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Notes
Location(s) and DNA Sequence
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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.
| Strain | Map location | Genome coordinates | Genome browsers | Sequence links |
|---|---|---|---|---|
|
MG1655 |
86.71 minutes |
MG1655: 4023011..4024504 |
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NC_012967: 4003459..4004952 |
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NC_012759: 3912680..3914173 |
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W3110 |
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W3110: 3611693..3610200 |
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DH10B: 4121931..4123424 |
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Notes
Sequence Features
See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.
| Feature Type | Strain | Genomic Location | Evidence | Reference | Notes |
|---|---|---|---|---|---|
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Notes
Alleles and Phenotypes
See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.
| Allele | Nt change(s) | AA change(s) | Phenotype: Type | Phenotype: Description | Reference | Availability | Comments |
|---|---|---|---|---|---|---|---|
|
ubiDG452R |
G452R |
(in AN66; inactive protein) |
Strain variation; seeded from UniProt:P0AAB4 | ||||
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ubiD410 |
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ubiD::Tn10dCam |
Mutagenesis rate |
Decreased stress-induced mutagenesis (SIM) phenotype. |
Parental Strain: SMR4562 Experimental Strain: SMR12313 |
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population. | |||
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SMR4562 yiaG-yfp FRT ubiD::Tn10dCam |
insertion |
SigmaS activity |
Decrease in SigmaS activity |
Parental Strain: SMR10582 Experimental Strain: SMR13098 |
See table S8 for full experimental data. | ||
|
CAG45114 ubiD::Tn10dCam |
insertion |
SigmaE activity |
Decrease in SigmaE activity |
Parental Strain: CAG45114 Experimental Strain: SMR15323 |
See table S11 for full experimental data. | ||
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Notes
Genetic Interactions
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| Interactor | Interaction | Allele | Score(s) | Reference(s) | Accessions | Notes |
|---|---|---|---|---|---|---|
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Notes
Genetic Resources
See Help:Gene_resources for help entering information into the Genetic Resources table.
| Resource | Resource Type | Source | Notes/Reference |
|---|---|---|---|
|
JW3819 |
Plasmid clone |
Status:Clone OK Primer 1:GCCGACGCCATGAAATATAACGA Primer 2:CCGGCGCTTTTACCGTTGTTAAA | |
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Kohara Phage |
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metEo-3079::Tn10 |
Linked marker |
est. P1 cotransduction: 60% [6] | |
|
Linked marker |
est. P1 cotransduction: 87% [6] | ||
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Notes
Accessions in Other Databases
See Help:Gene_accessions for help with entering information into the Gene Accessions table.
| Database | Accession | Notes |
|---|---|---|
|
Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Escherichia coli str. K-12 substr. MG1655 | ||
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Notes
Links
| Name | URL | Comments |
|---|---|---|
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References
See Help:References for how to manage references in EcoliWiki.
- ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
- ↑ 2.0 2.1 2.2 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
- ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed
- ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
- ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
- ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).
