ppdC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''ppdC''  
''ppdC''  
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!align=left {{table_heading_style}} |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
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''ECK2819, b2823, JW2791, ygdA''<ref name='LIB:Riley_2006'/>
''ECK2819, b2823, JW2791, ygdA''<ref name='LIB:Riley_2006'/>


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*[http://biocyc.org/ECOLI/sequence?object=EG11154 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 2857060..2857383<br />{{GBrowseFigureByCoord|2857060|2857383|REL606|NC_012967}}
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Synonyms:zgd-210::Tn10, zgf-210::Tn10  
Synonyms:zgd-210::Tn10, zgf-210::Tn10  


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Revision as of 05:19, 9 January 2010

{{#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 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

ppdC

Mnemonic
Synonyms

ECK2819, b2823, JW2791, ygdA[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

63.81 minutes 

MG1655: 2960786..2960463
gbrowse_img.php?coord=2960463..2960786&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2857060..2857383
gbrowse_img.php?coord=2857060..2857383&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2961420..2961097
gbrowse_img.php?coord=2961097..2961420&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3054656..3054333
gbrowse_img.php?coord=3054333..3054656&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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 Location Description
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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

ΔppdC (Keio:JW2791)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10183[3]

ppdC::Tn5KAN

PMID:12519969[4]

ASAP

At position 267 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20947

ppdC::Tn5KAN

PMID:12519969[4]

ASAP

At position 267 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20948

ΔppdC748::kan

PMID:16738554[2]

CGSC:102420


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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

JW2791

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTCAGCTTCCCTGAAGAATCA

Primer 2:CCtTGACGATTCGGGCAATGCAG

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 72% [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: % [6]
Synonyms:zgd-210::Tn10, zgf-210::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:EG11154

EchoBASE (EcoliWiki Page)

EchoBASE:EB1143

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2823

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3417

EcoGene (EcoliWiki Page)

EcoGene:EG11154

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PPDC

ASAP (EcoliWikiPage)

ASAP:ABE-0009257


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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. ↑ 2.0 2.1 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 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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 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).

Categories

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