dedD:Gene: Difference between revisions

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Convert to gbrowse_img.php extension.
Fixing Blattner deletion strains in alleles table.
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007643 dedD]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0007643 dedD::Tn5KAN-2] (FB20761)
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Insertion at nt 407 in Plus orientation
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PMID:12519969
PMID:15262929
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[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20761]
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At position 407 in Plus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20761
contains [[pKD46]]  
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Revision as of 21:29, 9 March 2011

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

dedD

Mnemonic

Downstream E. coli DNA

Synonyms

ECK2308, b2314, JW5378[1]

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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

52.35 minutes 

MG1655: 2429706..2429044
<gbrowseImage> name=NC_000913:2429044..2429706 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2375276..2374614
<gbrowseImage> name=NC_012967:2374614..2375276 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2314849..2315511
<gbrowseImage> name=NC_012759:2314849..2315511 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2437130..2436468
<gbrowseImage> name=AC_000091:2436468..2437130 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2521471..2520809
<gbrowseImage> name=NC_010473:2520809..2521471 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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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

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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

ΔdedD (Keio:JW5378)

deletion

deletion

PMID:16738554[2]

Shigen

dedD::Tn5KAN-2 (FB20761)

Insertion at nt 407 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB20761

contains pKD46

ΔdedD::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]


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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW5378

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGCAAGTAAGTTTCAGAATCG

Primer 2:CCATTCGGCGTATAGCCCATTAC

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[6]

est. P1 cotransduction: 19% [7]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[6]

est. P1 cotransduction: 3% [7]
Synonyms:zfb-1::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10218

EchoBASE (EcoliWiki Page)

EchoBASE:EB0214

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2314

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2859

EcoGene (EcoliWiki Page)

EcoGene:EG10218

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:DEDD

ASAP (EcoliWikiPage)

ASAP:ABE-0007643


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Notes

Links

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<protect>

References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  4. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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).

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