copA:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|{{Prettytable}}
{|   id="F46a9b1cc9cb14"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''copA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''copA''
Copper
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0478, b0484, JW0473, ybaR''<ref name='LIB:Riley_2006'/>, ybaR''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11533.F46a9b1cc9cb14&page=11533&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0478, b0484, JW0473, ybaR''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9b1cd20c43"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
Line 72: Line 76:
10.95 minutes&nbsp;
10.95 minutes&nbsp;
|
|
MG1655: 510603..508099<br />{{GBrowseFigureByCoord|507099|511603|ecoli|MG1655}}
MG1655: 510603..508099<br /><gbrowseImage>
name=NC_000913:508099..510603
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6260 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6260 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:507099..511603 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|507099|511603|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:508099..510603&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|508099|510603|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6260 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6260 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 483547..481043<br /><gbrowseImage>
name=NC_012967:481043..483547
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|481043|483547|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|481043|483547|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 410858..413362<br /><gbrowseImage>
name=NC_012759:410858..413362
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|410858|413362|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|410858|413362|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 86: Line 127:
&nbsp;
&nbsp;
|
|
W3110: 510603..508099<br />{{GBrowseFigureByCoord|507099|511603|ecoli_W3110|W3110}}  
W3110: 510603..508099<br /><gbrowseImage>
name=NC_007779:508099..510603
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|507099|511603|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|508099|510603|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 449934..447430<br /><gbrowseImage>
name=NC_010473:447430..449934
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:507099..511603 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|442422|454942|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:508099..510603&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|442422|454942|FASTA Dump}}
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
508102
|
Edman degradation
|
PMID:9868784<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46a9b1ce088f7"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
copAC113A
|
|
C113A
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-
|
copAC479A
|
|
C479A
|
|
Loss of copper resistance, transport and phosphoenzyme formation
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-
|
copAC481A,H
|
|
C481A,H
|
|
Loss of copper resistance, transport and phosphoenzyme formation
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-
|
copAC110A
|
|
C110A
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-
|
copA
|
|
|
|
|
|
|
Deletion
|-
|
copAC14A
|
|
C14A
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-
|
copAC17A
|
|
C17A
|
|
No effect
|
|
|
seeded from [http://www.uniprot.org/uniprot/Q59385 UniProt:Q59385]
|-  
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|
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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106906 CGSC8625]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106906 CGSC8625]<ref name='LIB:cgsc'/>  
Line 179: Line 375:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100374|CGSC:100374]]
[[cgscmutation:100374|CGSC:100374]]
|
|
   
   
|-
|
''copA(del)''
|
|
|
Sensitivity to
|
Sensitivity to antimicrobial agent Copper Ion.
|
PMID:10639134
|
Experimental Strain: LMG194
|
See growth curve in figure 2. 


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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW0473
JW0473
Line 214: Line 449:
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
Line 221: Line 456:


Primer 2:ccTTCCTTCGGTTTAAACCGCAGCAACCGG  
Primer 2:ccTTCCTTCGGTTTAAACCGCAGCAACCGG  
|-
|-
|
[[:Category:Kohara_Phage:4B10|4B10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=153 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7C12|7C12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=154 Genobase]
|
PMID:3038334
|-  
|
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[[gsk:Gene|gsk-3055::Tn10]]
[[gsk:Gene|gsk-3055::Tn10]]
Line 229: Line 482:
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zbb-30-55::TnlO, zba-3055::Tn10  
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/> <br />
|-
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10  
|-  
|
|
[[purK:Gene|purK79::Tn10]]
[[purK:Gene|purK79::Tn10]]
Line 238: Line 492:
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
CAG12171 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39380 CGSC7342]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 15% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:purE79::Tn10  
est. P1 cotransduction: 15% <ref name='LIB:Nichols_linked_Tn'/> <br />
|-
Synonyms:purE79::Tn10  
|-  
|
|
copA::kan
copA::kan
Line 247: Line 502:
CN2328
CN2328
|
|
[[PMID:11167016]]<ref name=PMID:11167016/>
PMID: 11167016  
|-
|-  
|
|
pCN2345
pCN2345
Line 256: Line 511:
copA with own promoter cloned into pBR322
copA with own promoter cloned into pBR322
|
|
[[PMID:11167016]]<ref name=PMID:11167016/>
PMID: 11167016  
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===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9b1cf393ac"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6260 EcoCyc:G6260]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3035 EchoBASE:EB3035]
EcoCyc:G6260
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0484 EcoliGenExpDB:b0484]
EcoGene:EG13246
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0604 ECOL199310CYC:C0604]
RegulonDB:ECK120002868
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13246 EcoGene:EG13246]
[http://www.ncbi.nlm.nih.gov/gene?term=946106 GeneID:946106]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YBAR ECOO157CYC:YBAR]
EchoBASE:EB3035
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001681&formSubmitReturn=1 ASAP:ABE-0001681] 
ASAP:ABE-0001681
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Categories===
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[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:cop genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:32, 19 September 2013

{{#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 Interactions 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

Copper

Synonyms

ECK0478, b0484, JW0473, ybaR[1], ybaR

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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
<gbrowseImage> name=NC_000913:508099..510603 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 483547..481043
<gbrowseImage> name=NC_012967:481043..483547 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 410858..413362
<gbrowseImage> name=NC_012759:410858..413362 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 510603..508099
<gbrowseImage> name=NC_007779:508099..510603 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 449934..447430
<gbrowseImage> name=NC_010473:447430..449934 source=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

Coding Start (SO:0000323)

MG1655

508102

Edman degradation

PMID:9868784[2]


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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

copAC113A

C113A

No effect

seeded from UniProt:Q59385

copAC479A

C479A

Loss of copper resistance, transport and phosphoenzyme formation

seeded from UniProt:Q59385

copAC481A,H

C481A,H

Loss of copper resistance, transport and phosphoenzyme formation

seeded from UniProt:Q59385

copAC110A

C110A

No effect

seeded from UniProt:Q59385

copA

Deletion

copAC14A

C14A

No effect

seeded from UniProt:Q59385

copAC17A

C17A

No effect

seeded from UniProt:Q59385

ΔcopA (Keio:JW0473)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8625[4]

ΔcopA1::kan

CGSC:77264

ΔcopA767::kan

PMID:16738554[3]

CGSC:100374

copA(del)

Sensitivity to

Sensitivity to antimicrobial agent Copper Ion.

PMID:10639134[5]

Experimental Strain: LMG194

See growth curve in figure 2.

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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

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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[6]

Status:Clone OK

Primer 1:gccTCACAAACTATCGACCTGACCCTGGAC

Primer 2:ccTTCCTTCGGTTTAAACCGCAGCAACCGG

4B10

Kohara Phage

Genobase

PMID:3038334[7]

7C12

Kohara Phage

Genobase

PMID:3038334[7]

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[4]

est. P1 cotransduction: 79% [8]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[4]

est. P1 cotransduction: 15% [8]
Synonyms:purE79::Tn10

copA::kan

Strain

CN2328

PMID:11167016[9]

pCN2345

Plasmid Clone

copA with own promoter cloned into pBR322

PMID:11167016[9]

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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

EcoCyc:G6260

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13246

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002868

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946106

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3035

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001681

Escherichia coli str. K-12 substr. MG1655

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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. ↑ Wasinger, VC & Humphery-Smith, I (1998) Small genes/gene-products in Escherichia coli K-12. FEMS Microbiol. Lett. 169 375-82 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ Rensing, C et al. (2000) CopA: An Escherichia coli Cu(I)-translocating P-type ATPase. Proc. Natl. Acad. Sci. U.S.A. 97 652-6 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  8. ↑ 8.0 8.1 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).
  9. ↑ 9.0 9.1 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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