yaeF: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="K46a9aa8a2bf48"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''yaeF''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yaeF''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0193, b0193, JW5016, yaeK''<ref name='LIB:Riley_2006'/>, yaeK''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48&page=10963&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0193, b0193, JW5016, yaeK''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48&page=10963&pagename={{FULLPAGENAMEE}} edit table]
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='126087'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9aa8aa46f0"  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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4.66 minutes&nbsp;
4.66 minutes&nbsp;
|
|
MG1655: 217003..216179<br />{{GBrowseFigureByCoord|215179|218003|ecoli|MG1655}}
MG1655: 217003..216179<br /><gbrowseImage>
name=NC_000913:216179..217003
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12138 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12138 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|215179|218003|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|215179|218003|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:216179..217003&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|216179|217003|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12138 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12138 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 219845..219021<br /><gbrowseImage>
name=NC_012967:219021..219845
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|219021|219845|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|219021|219845|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 216178..217002<br /><gbrowseImage>
name=NC_012759:216178..217002
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|216178|217002|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|216178|217002|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 217003..216179<br />{{GBrowseFigureByCoord|215179|218003|ecoli_W3110|W3110}}
W3110: 217003..216179<br /><gbrowseImage>
name=NC_007779:216179..217003
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:215179..218003 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|215179|218003|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:216179..217003&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|216179|217003|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 191107..190283<br /><gbrowseImage>
name=NC_010473:190283..191107
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|188635|192755|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|188635|192755|FASTA Dump}}
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='126088'
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.I46a9aa8b4da4c&page=10963&pagename={{FULLPAGENAMEE}} edit table] || ||
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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="V46a9aa8b8e7c5"  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
|-  
|-  
|
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&Delta;yaeF (Keio:JW5016)
''yaeF(del)'' (Keio:JW5016)
|
|
deletion
deletion
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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]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=109411 CGSC11130]<ref name='LIB:cgsc'/>  
|
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000655 yaeF::Tn5KAN-I-SceI] (FB20035)
|
Insertion at nt 155 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109411 CGSC11130]<ref name='LIB:cgsc'/>
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20035]
|
contains [[pKD46]]
|-
|
''yaeF(del)''::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|
   
   
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|
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[[PMID:12142427]]<ref name=PMID:12142427/>
PMID:12142427
|
|
[[cgscmutation:87198|CGSC:87198]]
[[cgscmutation:87198|CGSC:87198]]
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|-  
|-  
|
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''&#916;yaeF-2''
''yaeF-2(del)''
|
|


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|
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[[PMID:12142427]]<ref name=PMID:12142427/>
PMID:12142427
|
|
[[cgscmutation:87200|CGSC:87200]]
[[cgscmutation:87200|CGSC:87200]]
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|-  
|-  
|
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''&#916;yaeF-790::kan''
''yaeF-790(del)::kan''
|
|


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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:103480|CGSC:103480]]
[[cgscmutation:103480|CGSC:103480]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.V46a9aa8b8e7c5&page=10963&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}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.10963.E4e04c5dac3525-->
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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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JW5016
JW5016
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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:CCaCGGGTCAAACCAACAAAGCG  
Primer 2:CCaCGGGTCAAACCAACAAAGCG  
|-
|-
|
[[:Category:Kohara_Phage:6F5|6F5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=122 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10F9|10F9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=123 Genobase]
|
PMID:3038334
|-  
|
|
[[yadC:Gene|zad-220::Tn10]]
[[yadC:Gene|zad-220::Tn10]]
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|
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est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[yafC:Gene|yafC502::Tn10]]
[[yafC:Gene|yafC502::Tn10]]
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CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 57% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 57% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zae-502::Tn10


Synonyms:zae-502::Tn10
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===Notes===
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12138 EcoCyc:EG12138]
EcoCyc:EG12138
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2059 EchoBASE:EB2059]
EcoGene:EG12138
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0193 EcoliGenExpDB:b0193]
[http://www.ncbi.nlm.nih.gov/gene?term=944892 GeneID:944892]
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|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0234 ECOL199310CYC:C0234]
RegulonDB:ECK120002039
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12138 EcoGene:EG12138]
EchoBASE:EB2059
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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=YAEF ECOO157CYC:YAEF]
ASAP:ABE-0000655
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000655&formSubmitReturn=1 ASAP:ABE-0000655] 
|


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===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[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:yae genes]]
[[Category:yae genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:37, 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

yaeF

Mnemonic

Systematic nomenclature

Synonyms

ECK0193, b0193, JW5016, yaeK[1], yaeK

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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

4.66 minutes 

MG1655: 217003..216179
<gbrowseImage> name=NC_000913:216179..217003 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 219845..219021
<gbrowseImage> name=NC_012967:219021..219845 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 216178..217002
<gbrowseImage> name=NC_012759:216178..217002 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 217003..216179
<gbrowseImage> name=NC_007779:216179..217003 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 191107..190283
<gbrowseImage> name=NC_010473:190283..191107 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

yaeF(del) (Keio:JW5016)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC11130[3]

yaeF::Tn5KAN-I-SceI (FB20035)

Insertion at nt 155 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20035

contains pKD46

yaeF(del)::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

yaeF-1::FLKP2(lacZ,kan,Plac)

PMID:12142427[6]

CGSC:87198

yaeF-2(del)

PMID:12142427[6]

CGSC:87200

yaeF-790(del)::kan

PMID:16738554[2]

CGSC:103480


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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

JW5016

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGATAAACCAAAGGCGTACTG

Primer 2:CCaCGGGTCAAACCAACAAAGCG

6F5

Kohara Phage

Genobase

PMID:3038334[8]

10F9

Kohara Phage

Genobase

PMID:3038334[8]

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 2% [9]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 57% [9]
Synonyms:zae-502::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:EG12138

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12138

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944892

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002039

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2059

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000655

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. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  6. ↑ 6.0 6.1 Merlin, C et al. (2002) Tools for characterization of Escherichia coli genes of unknown function. J. Bacteriol. 184 4573-81 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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