recO:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|recO}}{{Tab On|Gene|recO}}{{Tab|Gene Product(s)|recO}}{{Tab|Expression|recO}}{{Tab|Evolution|recO}}{{Tab|On One Page|recO}}{{TabsBottom}}
{{Tab|Quickview|recO}}{{Tab On|Gene|recO}}{{Tab|Gene Product(s)|recO}}{{Tab|Expression|recO}}{{Tab|Evolution|recO}}{{Tab|On One Page|recO}}{{TabsBottom}}
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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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</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="U46a9e10d9d604"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''recO''  
''recO''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Recombination
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2563, b2565, JW2549''<ref name='LIB:Riley_2006'/>, JW2549''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15701.U46a9e10d9d604&page=15701&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2563, b2565, JW2549''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<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="H46a9e10e273a0"  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
|-
|-  
|
|
MG1655
MG1655
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58.19 minutes&nbsp;
58.19 minutes&nbsp;
|
|
MG1655: 2700491..2699763<br />{{GBrowseFigureByCoord|2698763|2701491|ecoli|MG1655}}
MG1655: 2700491..2699763<br /><gbrowseImage>
name=NC_000913:2699763..2700491
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10832 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10832 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2698763..2701491 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2698763|2701491|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2699763..2700491&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2699763|2700491|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10832 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10832 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2623961..2623233<br /><gbrowseImage>
name=NC_012967:2623233..2623961
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2623233|2623961|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2623233|2623961|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2585568..2586296<br /><gbrowseImage>
name=NC_012759:2585568..2586296
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2585568|2586296|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2585568|2586296|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2701125..2700397<br />{{GBrowseFigureByCoord|2699397|2702125|ecoli_W3110|W3110}}  
W3110: 2701125..2700397<br /><gbrowseImage>
name=NC_007779:2700397..2701125
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2699397|2702125|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|2700397|2701125|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2792256..2791528<br /><gbrowseImage>
name=NC_010473:2791528..2792256
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2699397..2702125 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2790072|2793712|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2700397..2701125&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2790072|2793712|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9e10ed4a88"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C46a9e10f2720c"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-
|
&Delta;recO (Keio:JW2549)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108309 CGSC10028]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;recO737::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102630|CGSC:102630]]
|
|-  
|
recO
|
deletion
|
 
|
Sensitivity to
|
increases sensitivity to [[Bicyclomycin]]
|
PMID:21357484
|
 
|
fig 2
|-
|
''recO1504''::Tn''5'' (KD2240)
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
Resistant to
|
|
&nbsp;
Mutation increases resistance to Thymineless Death (TLD). Figure 1.
|
|
&nbsp;
PMID:2848620
|
|
&nbsp;
 
|
|
&nbsp;
Parent Strain: KD2197
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15701.W4e04c22fa7a4c-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W4e04c22fa7a4c"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15701.W4e04c22fa7a4c&page=15701&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e10fd4f2d"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
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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:
Status:
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:7G4|7G4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=434 Genobase]
|
PMID:3038334
|-
|
[[hcaT:Gene|zfh-208::Tn10]]
|
Linked marker
|
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zff-208::Tn10
|-
|
[[nadB:Gene|nadB51::Tn10]]
|
Linked marker
|
CAG18480 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40090 CGSC7419]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/>
 
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<protect><!--Gene_resources_notes--></protect>
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10832 EcoCyc:EG10832] 
EcoCyc:EG10832
|
|
''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=EB0825 EchoBASE:EB0825] 
EcoGene:EG10832
|
|
''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=b2565 EcoliGenExpDB:b2565] 
RegulonDB:ECK120000823
|
|
''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=C3089 ECOL199310CYC:C3089]
[http://www.ncbi.nlm.nih.gov/gene?term=947038 GeneID:947038]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10832 EcoGene:EG10832] 
EchoBASE:EB0825
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=RECO ECOO157CYC:RECO] 
ASAP:ABE-0008438
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15701.C46a9e11077356&page=15701&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/17962 CGSC:17962] 
|
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===Notes===
===Notes===
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==Links==
==Links==
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==References==
==References==
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__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:rec genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 19 September 2013

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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

recO

Mnemonic

Recombination

Synonyms

ECK2563, b2565, JW2549[1], JW2549

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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

58.19 minutes 

MG1655: 2700491..2699763
<gbrowseImage> name=NC_000913:2699763..2700491 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2623961..2623233
<gbrowseImage> name=NC_012967:2623233..2623961 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2585568..2586296
<gbrowseImage> name=NC_012759:2585568..2586296 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2701125..2700397
<gbrowseImage> name=NC_007779:2700397..2701125 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2792256..2791528
<gbrowseImage> name=NC_010473:2791528..2792256 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

ΔrecO (Keio:JW2549)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10028[3]

ΔrecO737::kan

PMID:16738554[2]

CGSC:102630

recO

deletion

Sensitivity to

increases sensitivity to Bicyclomycin

PMID:21357484[4]

fig 2

recO1504::Tn5 (KD2240)

Resistant to

Mutation increases resistance to Thymineless Death (TLD). Figure 1.

PMID:2848620[5]

Parent Strain: KD2197

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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

Plasmid clone

Shigen

PMID:16769691[6]

Status:

Primer 1:

Primer 2:

7G4

Kohara Phage

Genobase

PMID:3038334[7]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[3]

est. P1 cotransduction: 22% [8]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[3]

est. P1 cotransduction: 72% [8]

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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:EG10832

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10832

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000823

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947038

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0825

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008438

Escherichia coli str. K-12 substr. MG1655

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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. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  5. ↑ Nakayama, K et al. (1988) Thymineless death in Escherichia coli mutants deficient in the RecF recombination pathway. Can. J. Microbiol. 34 905-7 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. ↑ 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).

Categories

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