yigA: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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{|{{Prettytable}}
{|  id="M46a9ff8f754ef"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''yigA''  
''yigA''
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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Systematic nomenclature<ref name='LIB:EcoGene'/>
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>
''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>, JW3783''
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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="X46a9ff90030b4"  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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86.08 minutes&nbsp;
86.08 minutes&nbsp;
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MG1655: 3993606..3994313<br />{{GBrowseFigureByCoord|3992606|3995313|ecoli|MG1655}}
MG1655: 3993606..3994313<br /><gbrowseImage>
name=NC_000913:3993606..3994313
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11201 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11201 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3992606..3995313 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3992606|3995313|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3993606..3994313&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3993606|3994313|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11201 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11201 EcoCyc Sequence Dump]  
|-
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[[REL606]]
|
 
|
NC_012967: 3957420..3958127<br /><gbrowseImage>
name=NC_012967:3957420..3958127
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3957420|3958127|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3957420|3958127|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 3641098..3640391<br />{{GBrowseFigureByCoord|3639391|3642098|ecoli_W3110|W3110}}
W3110: 3641098..3640391<br /><gbrowseImage>
name=NC_007779:3640391..3641098
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3639391..3642098 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3639391|3642098|GBrowse(W3110)}}
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3640391..3641098&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3640391|3641098|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="N46a9ff90bc018"  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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====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="Y46a9ff911227e"  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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Strain DH10B
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L156STOP
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Nonsense mutation
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PMID:18245285
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[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
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This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
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&Delta;yigA (Keio:JW3783)
&Delta;yigA (Keio:JW3783)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109031 CGSC10750]<ref name='LIB:cgsc'/>
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''&#916;yigA756::kan''
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PMID:16738554
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[[cgscmutation:105376|CGSC:105376]]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9ff91caa03"  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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JW3783
JW3783
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTACGCGTTCAATCCAACGCTC  
Primer 2:CCTACGCGTTCAATCCAACGCTC  
|-
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|
[[:Category:Kohara_Phage:12G1|12G1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=553 Genobase]
|
PMID:3038334
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[[ilvD:Gene|ilvD500::Tn10]]
[[ilvD:Gene|ilvD500::Tn10]]
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CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 18% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:ilv500::Tn10  
Synonyms:ilv500::Tn10  
|-
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metEo-3079::Tn10
metEo-3079::Tn10
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CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.


Synonyms:metE3079::Tn10
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The Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
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===Notes===
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|- {{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]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11201 EcoCyc:EG11201] 
EcoCyc:EG11201
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1186 EchoBASE:EB1186] 
EcoGene:EG11201
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3810 EcoliGenExpDB:b3810] 
RegulonDB:ECK120001181
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://BioCyc.org/ECOL199310/new-image?object=C4731 ECOL199310CYC:C4731]
[http://www.ncbi.nlm.nih.gov/gene?term=948359 GeneID:948359]
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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|
[http://ecogene.org/geneinfo.php?eg_id=EG11201 EcoGene:EG11201] 
EchoBASE:EB1186
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=YIGA ECOO157CYC:YIGA] 
ASAP:ABE-0012444
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yig genes]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:49, 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

yigA

Mnemonic

Systematic nomenclature

Synonyms

ECK3805, b3810, JW3783[1], JW3783

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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

86.08 minutes 

MG1655: 3993606..3994313
<gbrowseImage> name=NC_000913:3993606..3994313 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3957420..3958127
<gbrowseImage> name=NC_012967:3957420..3958127 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3641098..3640391
<gbrowseImage> name=NC_007779:3640391..3641098 source=W3110 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

Strain DH10B

L156STOP

Nonsense mutation

PMID:18245285[2]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔyigA (Keio:JW3783)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10750[4]

ΔyigA756::kan

PMID:16738554[3]

CGSC:105376


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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

JW3783

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAGCAACCAGGGGAAGAACT

Primer 2:CCTACGCGTTCAATCCAACGCTC

12G1

Kohara Phage

Genobase

PMID:3038334[6]

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[4]

est. P1 cotransduction: 18% [7]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[4]

est. P1 cotransduction: 59% [7]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG11201

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11201

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001181

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948359

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1186

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012444

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. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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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