ubiA: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="L46aa0574cdc21"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ubiA''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ubiA''
Ubiquinone
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4032, b4040, JW4000, cyr, sdgG?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, sdgG?''


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!{{table_heading_style}} |Synonyms
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''ECK4032, b4040, JW4000, cyr, sdgG?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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===Notes===
===Notes===
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<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aa05755cfe8"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
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MG1655
MG1655
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91.62 minutes&nbsp;
91.62 minutes&nbsp;
|
|
MG1655: 4251039..4251911<br />{{GBrowseFigureByCoord|4250039|4252911|ecoli|MG1655}}
MG1655: 4251039..4251911<br /><gbrowseImage>
name=NC_000913:4251039..4251911
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11370 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11370 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4250039..4252911 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4250039|4252911|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4251039..4251911&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4251039|4251911|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11370 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11370 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4231948..4232820<br /><gbrowseImage>
name=NC_012967:4231948..4232820
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4231948|4232820|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|4231948|4232820|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 4189884..4190756<br /><gbrowseImage>
name=NC_012759:4189884..4190756
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4189884|4190756|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4189884|4190756|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4256606..4257478<br />{{GBrowseFigureByCoord|4255606|4258478|ecoli_W3110|W3110}}  
W3110: 4256606..4257478<br /><gbrowseImage>
name=NC_007779:4256606..4257478
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4255606|4258478|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4256606|4257478|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 4350735..4351607<br /><gbrowseImage>
name=NC_010473:4350735..4351607
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4255606..4258478 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4348991|4353351|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4256606..4257478&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4348991|4353351|FASTA Dump}}
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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="Z46aa0576245b0"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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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="P46aa05766fc6a"  class=" tableEdit Gene_allele_table dataTable" 
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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
|-
|-  
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''ubiA::Tn''10''dCam
|
Insertion
|
 
|
Mutagenesis rate
|
Decrease in the rate of Stress Induced Mutagenesis (SIM).
|
PMID:23224554
|
Parent Strain: SMR4562 Experimental Strain: SMR12311
|
The mutation conferred a decrease in strong reduction in SIM with mutant frequency being reduced by 90 percent of the wild type. See table S3 for full experimental results. 
|-
|
''ubiA::Tn''10''dCam
|
Insertion
|
 
|
SDS-EDTA Sensitivity
|
Increase in SDS-EDTA sensitivity
|
PMID:23224554
|
Parent Strain: SMR4562 Experimental Strain: SMR12311
|
The mutation conferred an an increase in SDS-EDTA sensitivity relative to the wild type. See table S7 for a summary of results. 
|-
|
''ubiA::Tn''10''dCam
|
Insertion
|
 
|
 
|
Increased sensitivity toward UV radiation
|
PMID:23224554
|
Parent Strain: SMR4562 Experimental Strain: SMR12311
|
|
&Delta;ubiA (Keio:)
The mutation conferred an an increase in UV sensitivity relative to the wild type. See table S7 for a review of experimental results. 
|-
|
|
deletion
SMR4562 yiaG-yfp FRT ''ubiA''::Tn''10''dCam
|
|
deletion
Insertion
|
|


|
Sigma <sup>S</sup> activity
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Decrease in Sigma<sup>S</sup> activity
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PMID:23224554
|
Parental Strain: SMR10582
Experimental Strain: SMR14447
|
See table S8 for full experimental results. 
|-
|
CAG45114 ''ubiA''::Tn''10''dCam
|
Insertion
|
|


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
Sigma<sup>E</sup> activity
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] 
Decrease in sigma<sup>E</sup> activity
|
|
   
PMID:23224554
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Parental Strain: CAG45114
Experimental Strain: SMR15321
|
See table S11 for full experimental data.  
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E4e04c520c22bd"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW4000
JW4000
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[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
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Primer 2:CCGAAATGCCAGTAACTCATTGC  
Primer 2:CCGAAATGCCAGTAACTCATTGC  
|-
|-
|
[[:Category:Kohara_Phage:1F8|1F8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=634 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12B4|12B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=635 Genobase]
|
PMID:3038334
|-  
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[[malF:Gene|malF3089::Tn10]]
[[malF:Gene|malF3089::Tn10]]
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|
|
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 70% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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[[yjcS:Gene|zje-2241::Tn10]]
[[yjcS:Gene|zje-2241::Tn10]]
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|
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est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
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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="I46aa0577d8781"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11370 EcoCyc:EG11370] 
EcoCyc:EG11370
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1344 EchoBASE:EB1344] 
EcoGene:EG11370
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4040 EcoliGenExpDB:b4040] 
RegulonDB:ECK120001338
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5010 ECOL199310CYC:C5010]
[http://www.ncbi.nlm.nih.gov/gene?term=948540 GeneID:948540]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11370 EcoGene:EG11370] 
EchoBASE:EB1344
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=UBIA ECOO157CYC:UBIA] 
ASAP:ABE-0013229
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18639.I46aa0577d8781&page=18639&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/50 CGSC:50] 
|
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ubi genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 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

ubiA

Mnemonic

Ubiquinone

Synonyms

ECK4032, b4040, JW4000, cyr, sdgG?[1][2], sdgG?

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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

91.62 minutes 

MG1655: 4251039..4251911
<gbrowseImage> name=NC_000913:4251039..4251911 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4231948..4232820
<gbrowseImage> name=NC_012967:4231948..4232820 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4189884..4190756
<gbrowseImage> name=NC_012759:4189884..4190756 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4256606..4257478
<gbrowseImage> name=NC_007779:4256606..4257478 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4350735..4351607
<gbrowseImage> name=NC_010473:4350735..4351607 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
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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

ubiA::Tn10dCam

Insertion

Mutagenesis rate

Decrease in the rate of Stress Induced Mutagenesis (SIM).

PMID:23224554[3]

Parent Strain: SMR4562 Experimental Strain: SMR12311

The mutation conferred a decrease in strong reduction in SIM with mutant frequency being reduced by 90 percent of the wild type. See table S3 for full experimental results.

ubiA::Tn10dCam

Insertion

SDS-EDTA Sensitivity

Increase in SDS-EDTA sensitivity

PMID:23224554[3]

Parent Strain: SMR4562 Experimental Strain: SMR12311

The mutation conferred an an increase in SDS-EDTA sensitivity relative to the wild type. See table S7 for a summary of results.

ubiA::Tn10dCam

Insertion

Increased sensitivity toward UV radiation

PMID:23224554[3]

Parent Strain: SMR4562 Experimental Strain: SMR12311

The mutation conferred an an increase in UV sensitivity relative to the wild type. See table S7 for a review of experimental results.

SMR4562 yiaG-yfp FRT ubiA::Tn10dCam

Insertion

Sigma S activity

Decrease in SigmaS activity

PMID:23224554[3]

Parental Strain: SMR10582 Experimental Strain: SMR14447

See table S8 for full experimental results.

CAG45114 ubiA::Tn10dCam

Insertion

SigmaE activity

Decrease in sigmaE activity

PMID:23224554[3]

Parental Strain: CAG45114 Experimental Strain: SMR15321

See table S11 for full experimental data.

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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

JW4000

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGAGTGGAGTCTGACGCAGAA

Primer 2:CCGAAATGCCAGTAACTCATTGC

1F8

Kohara Phage

Genobase

PMID:3038334[5]

12B4

Kohara Phage

Genobase

PMID:3038334[5]

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[6]

est. P1 cotransduction: 70% [7]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[6]

est. P1 cotransduction: 7% [7]

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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:EG11370

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11370

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001338

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948540

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1344

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013229

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 3.4 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  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 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
  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).

Categories

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