ppiD:Gene: Difference between revisions

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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
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[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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zaj-3054::Tn10
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Insertion at 461,486 bp in [[MG1655]] (NC_000913)
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adapted from Nichols ''et al.''<ref name ='LIB:Nichols_linked_Tn'/>
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CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
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Synonyms: zba-3054::Tn10
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Revision as of 21:22, 28 July 2007

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

Nomenclature

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Standard name

ppiD

Mnemonic
Synonyms

ECK0435, b0441, JW0431, ybaU[1]

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

Notes

Location(s) and DNA Sequence

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Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

9.94 minutes 

MG1655: 461139..463010
gbrowse_img.php?coord=460139..464010&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 461139..463010
gbrowse_img.php?coord=460139..464010&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

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Feature type Location Description
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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔppiD (Keio:JW0431)

deletion

deletion

PMID:16738554[2]

Shigen

zaj-3054::Tn10

Insertion at 461,486 bp in MG1655 (NC_000913)

adapted from Nichols et al.[3]

CAG12017 = CGSC7339[4]

Synonyms: zba-3054::Tn10

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

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Resource Resource Type Source Notes/Reference

JW0431

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCATGGACAGCTTACGCACGGC

Primer 2:CCTTGCTGTTCCAGCGCATCGCC

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[4]

est. P1 cotransduction: 32% [3]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[4]

est. P1 cotransduction: 18% [3]

Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

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

Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G6242

EchoBASE (EcoliWiki Page)

EchoBASE:EB3038

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0441

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0557

EcoGene (EcoliWiki Page)

EcoGene:EG13249

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBAU

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

Notes

Links

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Name URL Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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. ↑ 3.0 3.1 3.2 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).
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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


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