artQ:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|artQ}}{{Tab On|Gene|artQ}}{{Tab|Gene Product(s)|artQ}}{{Tab|Expression|artQ}}{{Tab|Evolution|artQ}}{{Tab|On One Page|artQ}}{{TabsBottom}}
{{Tab|Quickview|artQ}}{{Tab On|Gene|artQ}}{{Tab|Gene Product(s)|artQ}}{{Tab|Expression|artQ}}{{Tab|Evolution|artQ}}{{Tab|On One Page|artQ}}{{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>
==Nomenclature==
==Nomenclature==
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{|   id="P46a9ba60340a6"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''artQ''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''artQ''
Arginine transport
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0853, b0862, JW0846''<ref name='LIB:Riley_2006'/>, JW0846''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12283.P46a9ba60340a6&page=12283&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0853, b0862, JW0846''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="Z46a9ba60ac808"  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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19.41 minutes&nbsp;
19.41 minutes&nbsp;
|
|
MG1655: 901473..900757<br />{{GBrowseFigureByCoord|899757|902473|ecoli|MG1655}}
MG1655: 901473..900757<br /><gbrowseImage>
name=NC_000913:900757..901473
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11626 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11626 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:899757..902473 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|899757|902473|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:900757..901473&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|900757|901473|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11626 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11626 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 918957..918241<br /><gbrowseImage>
name=NC_012967:918241..918957
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|918241|918957|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|918241|918957|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 803725..804441<br /><gbrowseImage>
name=NC_012759:803725..804441
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|803725|804441|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|803725|804441|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 902672..901956<br />{{GBrowseFigureByCoord|900956|903672|ecoli_W3110|W3110}}  
W3110: 902672..901956<br /><gbrowseImage>
name=NC_007779:901956..902672
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|900956|903672|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:900956..903672 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|901956|902672|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:901956..902672&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 955401..954685<br /><gbrowseImage>
name=NC_010473:954685..955401
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|953253|956833|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|953253|956833|FASTA Dump}}
 
|- class="tableEdit_footer"
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<!--Location_notes--></protect>
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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="Q46a9ba6156854"  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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<protect><!--Sequence_notes--></protect>
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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="U46a9ba6196e4b"  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;artQ (Keio:JW0846)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107163 CGSC8882]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0002933 artQ::Tn5KAN-2] (FB20245)
|
Insertion at nt 320 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20245]
|
does not contain [[pKD46]]
|-  
|
''&#916;artQ763::kan''
|
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
|
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&nbsp;
 
|
|
&nbsp;
PMID:16738554
|
|
&nbsp;
[[cgscmutation:100096|CGSC:100096]]
|
|
&nbsp;
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12283.U46a9ba6196e4b&page=12283&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R4e04b7c98e9e2"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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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="J46a9ba6240eb5"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0846
JW0846
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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:CCGCTGGGCCTCCGCTCAAAACG  
Primer 2:CCGCTGGGCCTCCGCTCAAAACG  
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[[:Category:Kohara_Phage:14H6|14H6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=211 Genobase]
|
PMID:3038334
|-
|
zbh-29::Tn10
|
Linked marker
|
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10
|-
|
zca-1230::Tn10
|
Linked marker
|
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::Tn10
 
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9ba62ca9cd"  class=" tableEdit Gene_accessions_table" 
|- {{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=EG11626 EcoCyc:EG11626] 
EcoCyc:EG11626
|
|
''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=EB1583 EchoBASE:EB1583] 
EcoGene:EG11626
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0862 EcoliGenExpDB:b0862]
[[RegulonDB]]
|
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RegulonDB:ECK120001574
|-
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
|-  
[http://BioCyc.org/ECOL199310/new-image?object=C0995 ECOL199310CYC:C0995]
|
|-
|
|
[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=EG11626 EcoGene:EG11626]
[http://www.ncbi.nlm.nih.gov/gene?term=949046 GeneID:949046]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=ARTQ ECOO157CYC:ARTQ] 
EchoBASE:EB1583
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/31670 CGSC:31670] 
ASAP:ABE-0002933
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:art genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

artQ

Mnemonic

Arginine transport

Synonyms

ECK0853, b0862, JW0846[1], JW0846

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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

19.41 minutes 

MG1655: 901473..900757
<gbrowseImage> name=NC_000913:900757..901473 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 918957..918241
<gbrowseImage> name=NC_012967:918241..918957 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 803725..804441
<gbrowseImage> name=NC_012759:803725..804441 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 902672..901956
<gbrowseImage> name=NC_007779:901956..902672 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 955401..954685
<gbrowseImage> name=NC_010473:954685..955401 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

ΔartQ (Keio:JW0846)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8882[3]

artQ::Tn5KAN-2 (FB20245)

Insertion at nt 320 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20245

does not contain pKD46

ΔartQ763::kan

PMID:16738554[2]

CGSC:100096


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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

JW0846

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAATGAATTTTTTCCTTTAGC

Primer 2:CCGCTGGGCCTCCGCTCAAAACG

14H6

Kohara Phage

Genobase

PMID:3038334[6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[3]

est. P1 cotransduction: % [7]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[3]

est. P1 cotransduction: 13% [7]
Synonyms:zbj-1230::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:EG11626

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11626

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001574

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:949046

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1583

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002933

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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  6. ↑ 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
  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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