copA:Gene: Difference between revisions

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Fixing REL gene coord display.
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!align=left |Standard name
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''copA''  
''copA''  
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0478, b0484, JW0473, ybaR''<ref name='LIB:Riley_2006'/>
''ECK0478, b0484, JW0473, ybaR''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 481043..483547<br />{{GBrowseFigureByCoord|481043|483547|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|481043|483547|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|481043|483547|GBrowse (REL606)}}
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Revision as of 20:15, 21 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

copA

Mnemonic
Synonyms

ECK0478, b0484, JW0473, ybaR[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

10.95 minutes 

MG1655: 510603..508099
gbrowse_img.php?coord=508099..510603&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 483547..481043
gbrowse_img.php?coord=481043..483547&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 510603..508099
gbrowse_img.php?coord=508099..510603&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 449934..447430
gbrowse_img.php?coord=447430..449934&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

ΔcopA (Keio:JW0473)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8625[3]

ΔcopA1::kan

CGSC:77264

ΔcopA767::kan

PMID:16738554[2]

CGSC:100374


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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

JW0473

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:gccTCACAAACTATCGACCTGACCCTGGAC

Primer 2:ccTTCCTTCGGTTTAAACCGCAGCAACCGG

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 79% [5]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 15% [5]
Synonyms:purE79::Tn10

copA::kan

Strain

CN2328

PMID:11167016[6]

pCN2345

Plasmid Clone

copA with own promoter cloned into pBR322

PMID:11167016[6]

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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:G6260

EchoBASE (EcoliWiki Page)

EchoBASE:EB3035

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0484

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0604

EcoGene (EcoliWiki Page)

EcoGene:EG13246

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBAR

ASAP (EcoliWikiPage)

ASAP:ABE-0001681


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Notes

Links

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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. ↑ 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
  5. ↑ 5.0 5.1 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).
  6. ↑ 6.0 6.1 Petersen, C & Møller, LB (2000) Control of copper homeostasis in Escherichia coli by a P-type ATPase, CopA, and a MerR-like transcriptional activator, CopR. Gene 261 289-98 PubMed

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