dnaX: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="G46a9b1755630e"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''dnaX''
 
|-
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
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''ECK0464, b0470, JW0459, dnaZ''<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="I46a9b1760848b"  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
|-
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MG1655
MG1655
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10.59 minutes&nbsp;
10.59 minutes&nbsp;
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MG1655: 491316..493247<br />{{GBrowseFigureByCoord|490316|494247|ecoli|MG1655}}
MG1655: 491316..493247<br /><gbrowseImage>
name=NC_000913:491316..493247
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10245 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10245 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|490316|494247|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|490316|494247|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|491316|493247|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|491316|493247|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10245 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10245 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 464159..466090<br /><gbrowseImage>
name=NC_012967:464159..466090
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|464159|466090|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|464159|466090|FASTA Dump}}
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[[BW2952]]
|
 
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NC_012759: 394075..396006<br /><gbrowseImage>
name=NC_012759:394075..396006
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|394075|396006|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|394075|396006|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 491316..493247<br />{{GBrowseFigureByCoord|490316|494247|ecoli_W3110|W3110}}  
W3110: 491316..493247<br /><gbrowseImage>
name=NC_007779:491316..493247
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|490316|494247|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|491316|493247|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 430647..432578<br /><gbrowseImage>
name=NC_010473:430647..432578
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_W3110|AC_000091|490316|494247|GBrowse(W3110)}}  
{{GBrowseLink|DH10B|NC_010473|426785|436440|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|491316|493247|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|426785|436440|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]]
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491319
|
Edman degradation
|
PMID:3283125<br />
|
 
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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="Y46a9b1775c6d3"  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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ts growth.  Fast stop DNA replication arrest at 44°
ts growth.  Fast stop DNA replication arrest at 44°
|
|
[[PMID:16430690]]
PMID:16430690
[[PMID:8376347]]
PMID:8376347
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Other
 
|
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Weak mutator in mismatch repair deficient strain
Weak mutator in mismatch repair deficient strain
|
|
[[PMID:16430690]]
PMID:16430690
|
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G118D
|
|
 
Growth Phenotype
|
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Ts for replication and growth
|
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PMID:8376347
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[[cgscmutation:10601|CGSC:10601]]
[[cgscmutation:10601|CGSC:10601]]
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failure to suppress parE10 when overexpressed
failure to suppress parE10 when overexpressed
|
|
[[PMID:12535532]]<ref name=PMID:12535532/>
PMID:12535532
|
|


|
|
   
   
|-
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''dnaX(Ts)''
|
|
G118D
|
Growth Phenotype
|
temperature sensitive for replication and growth
|
PMID:12775696
|
|
phenotype suppressed by mutations in DnaA


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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
The dnaX locus was identified by the J, Walker lab<ref name='PMID:391641'/> as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in [[dnaZ]]<ref name='PMID:333440'/>.
The dnaX locus was identified by the J, Walker lab<ref name='PMID:391641'/> as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in [[dnaZ]].<ref name='PMID:333440'/>
 
 
==Genetic Interactions==
{{BacktoTop}}
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
 
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0459
JW0459
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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:CCAATGGGGCGGATACTTTCTTC  
Primer 2:CCAATGGGGCGGATACTTTCTTC  
|-
|-
|
[[:Category:Kohara_Phage:8C4|8C4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=151 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12H5|12H5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=152 Genobase]
|
PMID:3038334
|-  
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[[ppiD:Gene|zaj-3054::Tn10]]
[[ppiD:Gene|zaj-3054::Tn10]]
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CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zba-3054::Tn10  
Synonyms:zba-3054::Tn10  
|-
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[[gsk:Gene|gsk-3055::Tn10]]
[[gsk:Gene|gsk-3055::Tn10]]
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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: 72% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10


Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
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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="X46a9b17929b14"  class=" tableEdit Gene_accessions_table"   
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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=EG10245 EcoCyc:EG10245]
EcoCyc:EG10245
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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=EB0241 EchoBASE:EB0241]
EcoGene:EG10245
|
|
''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=b0470 EcoliGenExpDB:b0470]
RegulonDB:ECK120000239
|
|
''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=C0589 ECOL199310CYC:C0589]
[http://www.ncbi.nlm.nih.gov/gene?term=945105 GeneID:945105]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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|
[http://ecogene.org/geneinfo.php?eg_id=EG10245 EcoGene:EG10245]
EchoBASE:EB0241
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|
''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=DNAX ECOO157CYC:DNAX]
ASAP:ABE-0001633
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/838 CGSC:838]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001633&formSubmitReturn=1 ASAP:ABE-0001633]
|


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:dna genes]]
[[Category:dna genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:18, 22 April 2014

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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
Mnemonic
Synonyms


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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

10.59 minutes 

MG1655: 491316..493247
<gbrowseImage> name=NC_000913:491316..493247 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 464159..466090
<gbrowseImage> name=NC_012967:464159..466090 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 394075..396006
<gbrowseImage> name=NC_012759:394075..396006 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 491316..493247
<gbrowseImage> name=NC_007779:491316..493247 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 430647..432578
<gbrowseImage> name=NC_010473:430647..432578 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

491319

Edman degradation

PMID:3283125[1]


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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

dnaX36

E601K

Growth Phenotype

ts growth. Fast stop DNA replication arrest at 44°

PMID:16430690[2] PMID:8376347[3]

Affects Tau but not Gamma

dnaX36

Weak mutator in mismatch repair deficient strain

PMID:16430690[2]

dnaX0

CGSC:10600

dnaX2016

G118D

Growth Phenotype

Ts for replication and growth

PMID:8376347[3]

CGSC:10601

dnaX36(ts)

temperature sensitive

CGSC:10704

dnaXE145A

E145A

failure to suppress parE10 when overexpressed

PMID:12535532[4]

dnaX(Ts)

G118D

Growth Phenotype

temperature sensitive for replication and growth

PMID:12775696[5]

phenotype suppressed by mutations in DnaA

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Notes

The dnaX locus was identified by the J, Walker lab[6] as the site of one of several ts mutations in strain SG133, which was originally thought to contain a single mutation in dnaZ.[7]


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

JW0459

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCAGTTATCAGGTCTTAGCCCG

Primer 2:CCAATGGGGCGGATACTTTCTTC

8C4

Kohara Phage

Genobase

PMID:3038334[9]

12H5

Kohara Phage

Genobase

PMID:3038334[9]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[10]

est. P1 cotransduction: 28% [11]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[10]

est. P1 cotransduction: 72% [11]
Synonyms:zbb-30-55::TnlO, zba-3055::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

EcoCyc:EG10245

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10245

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000239

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945105

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0241

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001633

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. ↑ Maki, S & Kornberg, A (1988) DNA polymerase III holoenzyme of Escherichia coli. I. Purification and distinctive functions of subunits tau and gamma, the dnaZX gene products. J. Biol. Chem. 263 6547-54 PubMed
  2. ↑ 2.0 2.1 Pham, PT et al. (2006) Mutator mutants of Escherichia coli carrying a defect in the DNA polymerase III tau subunit. Mol. Microbiol. 59 1149-61 PubMed
  3. ↑ 3.0 3.1 Blinkova, A et al. (1993) The Escherichia coli DNA polymerase III holoenzyme contains both products of the dnaX gene, tau and gamma, but only tau is essential. J. Bacteriol. 175 6018-27 PubMed
  4. ↑ Espeli, O et al. (2003) Temporal regulation of topoisomerase IV activity in E. coli. Mol. Cell 11 189-201 PubMed
  5. ↑ Blinkova, A et al. (2003) Suppression of temperature-sensitive chromosome replication of an Escherichia coli dnaX(Ts) mutant by reduction of initiation efficiency. J. Bacteriol. 185 3583-95 PubMed
  6. ↑ Henson, JM et al. (1979) Isolation and characterization of dnaX and dnaY temperature-sensitive mutants of Escherichia coli. Genetics 92 1041-59 PubMed
  7. ↑ Sevastopoulos, CG et al. (1977) Large-scale automated isolation of Escherichia coli mutants with thermosensitive DNA replication. Proc. Natl. Acad. Sci. U.S.A. 74 3485-9 PubMed
  8. ↑ 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
  9. ↑ 9.0 9.1 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
  10. ↑ 10.0 10.1 CGSC: The Coli Genetics Stock Center
  11. ↑ 11.0 11.1 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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