envR: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="Q46a9f198980ce"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''envR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''envR''
Envelope
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3251, b3264, JW3232, acrS, yhdK''<ref name='LIB:Riley_2006'/>, yhdK''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17077.Q46a9f198980ce&page=17077&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3251, b3264, JW3232, acrS, yhdK''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='144432'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9f199253b6"  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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73.51 minutes&nbsp;
73.51 minutes&nbsp;
|
|
MG1655: 3411487..3410825<br />{{GBrowseFigureByCoord|3409825|3412487|ecoli|MG1655}}
MG1655: 3411487..3410825<br /><gbrowseImage>
name=NC_000913:3410825..3411487
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11741 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11741 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3409825..3412487 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3409825|3412487|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3410825..3411487&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3410825|3411487|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11741 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11741 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3341356..3340694<br /><gbrowseImage>
name=NC_012967:3340694..3341356
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3340694|3341356|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3340694|3341356|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3297973..3298635<br /><gbrowseImage>
name=NC_012759:3297973..3298635
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3297973|3298635|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3297973|3298635|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3413320..3412658<br />{{GBrowseFigureByCoord|3411658|3414320|ecoli_W3110|W3110}}  
W3110: 3413320..3412658<br /><gbrowseImage>
name=NC_007779:3412658..3413320
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3411658|3414320|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3412658|3413320|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 3509232..3508570<br /><gbrowseImage>
name=NC_010473:3508570..3509232
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3411658..3414320 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3507246|3510556|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3412658..3413320&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3507246|3510556|FASTA Dump}}
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===Notes===
===Notes===
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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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{|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="Q46a9f19a2d7cd"  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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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108726 CGSC10445]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108726 CGSC10445]<ref name='LIB:cgsc'/>  
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010712 envR::Tn5KAN-I-SceI] (FB21089)
|
Insertion at nt 577 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21089]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0010712 envR::Tn5KAN-I-SceI] (FB21090)
|
Insertion at nt 577 in Minus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21090]
|
does not contain [[pKD46]]
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|N-Acetyl-D-glucosamine]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|b-Methyl-D-glucoside]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Hydroxybutyrate]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
|
|-
|
&Delta;envR::kan
|
deletion
|
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Aspartate]]
|
PMID:16095938
|
|
|
   
   
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:100722|CGSC:100722]]
[[cgscmutation:100722|CGSC:100722]]
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<protect><!--Alleles_notes--></protect>
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===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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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3232
JW3232
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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:CCCATGACACTTAATTCATTCGT  
Primer 2:CCCATGACACTTAATTCATTCGT  
|-
|-
|
[[:Category:Kohara_Phage:6G3|6G3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=529 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6G9|6G9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=530 Genobase]
|
PMID:3038334
|-  
|
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[[yhcF:Gene|zhc-6::Tn10]]
[[yhcF:Gene|zhc-6::Tn10]]
Line 212: Line 486:
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
CAG12153 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38765 CGSC7442]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 12% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zha-6::Tn10  
Synonyms:zha-6::Tn10  
|-
|-  
|
|
[[acrF:Gene|acrF3083::Tn10]]
[[acrF:Gene|acrF3083::Tn10]]
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CAG12075 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40247 CGSC7447]<ref name='LIB:cgsc'/>
CAG12075 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40247 CGSC7447]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 88% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10


Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11741 EcoCyc:EG11741] 
EcoCyc:EG11741
|
|
''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=EB1692 EchoBASE:EB1692] 
EcoGene:EG11741
|
|
''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=b3264 EcoliGenExpDB:b3264] 
RegulonDB:ECK120001680
|
|
''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=C4030 ECOL199310CYC:C4030]
[http://www.ncbi.nlm.nih.gov/gene?term=947704 GeneID:947704]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11741 EcoGene:EG11741] 
EchoBASE:EB1692
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=ENVR ECOO157CYC:ENVR] 
ASAP:ABE-0010712
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
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[[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:env genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

envR

Mnemonic

Envelope

Synonyms

ECK3251, b3264, JW3232, acrS, yhdK[1], yhdK

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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

73.51 minutes 

MG1655: 3411487..3410825
<gbrowseImage> name=NC_000913:3410825..3411487 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3341356..3340694
<gbrowseImage> name=NC_012967:3340694..3341356 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3297973..3298635
<gbrowseImage> name=NC_012759:3297973..3298635 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3413320..3412658
<gbrowseImage> name=NC_007779:3412658..3413320 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3509232..3508570
<gbrowseImage> name=NC_010473:3508570..3509232 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

ΔenvR (Keio:JW3232)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10445[3]

envR::Tn5KAN-I-SceI (FB21089)

Insertion at nt 577 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21089

contains pKD46

envR::Tn5KAN-I-SceI (FB21090)

Insertion at nt 577 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB21090

does not contain pKD46

ΔenvR::kan

deletion

Biolog:respiration

unable to respire N-Acetyl-D-glucosamine

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire b-Methyl-D-glucoside

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[5]

ΔenvR::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[5]

ΔenvR782::kan

PMID:16738554[2]

CGSC:100722


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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

JW3232

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGCAAAAAGAACCAAAGCCGA

Primer 2:CCCATGACACTTAATTCATTCGT

6G3

Kohara Phage

Genobase

PMID:3038334[7]

6G9

Kohara Phage

Genobase

PMID:3038334[7]

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[3]

est. P1 cotransduction: 12% [8]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[3]

est. P1 cotransduction: 88% [8]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG11741

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11741

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001680

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947704

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1692

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010712

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 5.2 5.3 5.4 5.5 5.6 5.7 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. ↑ 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. ↑ 7.0 7.1 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
  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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