phnE:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
{{Tab|Quickview|phnE}}{{Tab On|Gene|phnE}}{{Tab|Gene Product(s)|phnE}}{{Tab|Expression|phnE}}{{Tab|Evolution|phnE}}{{Tab|On One Page|phnE}}{{TabsBottom}}
{{Tab|Quickview|phnE}}{{Tab On|Gene|phnE}}{{Tab|Gene Product(s)|phnE}}{{Tab|Expression|phnE}}{{Tab|Evolution|phnE}}{{Tab|On One Page|phnE}}{{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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==Nomenclature==
==Nomenclature==
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{|  id="F46aa0722018e1"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''phnE''  
''phnE''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4096, b4103, JW4064, ECK4097, b4104, JW4065''<ref name='LIB:Riley_2006'/>
''ECK4096, b4103, JW4064, ECK4097, b4104, JW4065''<ref name='LIB:Riley_2006'/>
|-
 
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<!--Nomenclature_notes--></protect>
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===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="H46aa072285484"  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
|-
|-  
|
|
MG1655
MG1655
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93.12 minutes, 93.12 minutes, 93.12 minutes&nbsp;
93.12 minutes, 93.12 minutes, 93.12 minutes&nbsp;
|
|
MG1655: 4320834..4320466<br />{{GBrowseFigureByCoord|4319466|4321834|ecoli|MG1655}}
MG1655: 4320834..4320466<br /><gbrowseImage>
name=NC_000913:4320466..4320834
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11283 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11283 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4319466..4321834 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4319466|4321834|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4320466..4320834&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4320466|4320834|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11283 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11283 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4302083..4301265<br /><gbrowseImage>
name=NC_012967:4301265..4302083
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4301265|4302083|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4301265|4302083|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4327489..4327121<br />{{GBrowseFigureByCoord|4326121|4328489|ecoli_W3110|W3110}}
W3110: 4327489..4327121<br /><gbrowseImage>
name=NC_007779:4327121..4327489
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4326121..4328489 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4326121|4328489|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4327121..4327489&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4327121|4327489|FASTA Dump}}
|-
|-  
|
|
MG1655
MG1655
|
|
93.12 minutes, 93.12 minutes, 93.12 minutes&nbsp;
93.12 minutes, 93.12 minutes, 93.12 minutes 
|
|
MG1655: 4321304..4320684<br />{{GBrowseFigureByCoord|4319684|4322304|ecoli|MG1655}}
MG1655: 4321304..4320684<br /><gbrowseImage>
name=NC_000913:4320684..4321304
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11283 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11283 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4319684..4322304 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4319684|4322304|GBrowse (MG1655)}}<br />
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4320684..4321304&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|MG1655|NC_000913|4320684|4321304|FASTA Dump}}<br />
*[http://biocyc.org/ECOLI/sequence?object=EG11283 EcoCyc Sequence Dump]
|-  
|-
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|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4327959..4327339<br />{{GBrowseFigureByCoord|4326339|4328959|ecoli_W3110|W3110}}
W3110: 4327959..4327339<br /><gbrowseImage>
name=NC_007779:4327339..4327959
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4326339..4328959 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4326339|4328959|GBrowse (W3110)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4327339..4327959&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|W3110|NC_007779|4327339|4327959|FASTA Dump}}<br \>
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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="T46aa072450fae"  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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====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="U46aa07249c5e0"  class=" tableEdit Gene_allele_table dataTable" 
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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
|-class='sortbottom'
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''phnE(del)'' (Keio:JW4064)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=109204 CGSC10923]<ref name='LIB:cgsc'/>
|
|-  
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''phnE(del)'' (Keio:JW4065)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=109204 CGSC10923]<ref name='LIB:cgsc'/>
|
|-
|
''phnE728(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102334|CGSC:102334]]
|
|-
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''phnE729(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102336|CGSC:102336]]
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===




==Genetic Resources==
 
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==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H4e04c1068303e"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<protect><!--Gene_resources_notes--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===
===Notes===


==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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|
JW4064
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691


==Accessions in Other Databases==
Status:Clone OK
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<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY. Use the edit table link under the table. ***  -->
Primer 1:GCCCTGGCGCTGTTTATCCACAC
{|class = 'sortable' {{Prettytable}} id='29090'
 
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Primer 2:CCGATAAAGTGCTTACGCAACCG
!Database!!Accession!!Notes
|-  
|-
|
[[:Category:Kohara_Phage:10H5|10H5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=642 Genobase]
|
PMID:3038334
|-  
|
[[:Category:Kohara_Phage:12H2|12H2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=643 Genobase]
|
PMID:3038334
|-  
|
[[:Category:Kohara_Phage:2C12|2C12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=644 Genobase]
|
PMID:3038334
|-  
|
JW4065
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
Plasmid clone
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11283 EcoCyc:EG11283]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
PMID:16769691
|-
 
Status:Clone OK
 
Primer 1:GCCCCGGATGCGGTGCAAGCACC
 
Primer 2:CCtCTGTGGCAGCACGCCGTAGA
|-
|
[[yjcS:Gene|zje-2241::Tn10]]
|
Linked marker
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
CAG18427 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40603 CGSC7481]<ref name='LIB:cgsc'/>
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1260 EchoBASE:EB1260] 
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
|
[[cadB:Gene|cadB2231::Tn10]]
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
Linked marker
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4104 EcoliGenExpDB:b4104] 
CAG18488 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40596 CGSC7479]<ref name='LIB:cgsc'/>
|
|
   
est. P1 cotransduction: 23% <ref name='LIB:Nichols_linked_Tn'/> <br />
|-
Synonyms:zjd-2231::Tn10
 
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===Notes===
 
 
==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="S46aa07275bfed"  class=" tableEdit Gene_accessions_table" 
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!|Database!!Accession!!Notes
|-  
|
|
[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=EG11283 EcoGene:EG11283]
[http://www.ncbi.nlm.nih.gov/gene?term=948625 GeneID:948625]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5109 ECOL199310CYC:C5109] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=PHNE ECOO157CYC:PHNE] 
EchoBASE:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/34550 CGSC:34550] 
ASAP:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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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:phn genes]][[Category:Gene_List:REL606]]

Latest revision as of 20:51, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

phnE

Mnemonic
Synonyms

ECK4096, b4103, JW4064, ECK4097, b4104, JW4065[1]

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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

93.12 minutes, 93.12 minutes, 93.12 minutes 

MG1655: 4320834..4320466
<gbrowseImage> name=NC_000913:4320466..4320834 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4302083..4301265
<gbrowseImage> name=NC_012967:4301265..4302083 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4327489..4327121
<gbrowseImage> name=NC_007779:4327121..4327489 source=W3110 preset=GeneLocation </gbrowseImage>

MG1655

93.12 minutes, 93.12 minutes, 93.12 minutes 

MG1655: 4321304..4320684
<gbrowseImage> name=NC_000913:4320684..4321304 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4327959..4327339
<gbrowseImage> name=NC_007779:4327339..4327959 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

phnE(del) (Keio:JW4064)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10923[3]

phnE(del) (Keio:JW4065)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10923[3]

phnE728(del)::kan

PMID:16738554[2]

CGSC:102334

phnE729(del)::kan

PMID:16738554[2]

CGSC:102336


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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

JW4064

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCTGGCGCTGTTTATCCACAC

Primer 2:CCGATAAAGTGCTTACGCAACCG

10H5

Kohara Phage

Genobase

PMID:3038334[5]

12H2

Kohara Phage

Genobase

PMID:3038334[5]

2C12

Kohara Phage

Genobase

PMID:3038334[5]

JW4065

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCCGGATGCGGTGCAAGCACC

Primer 2:CCtCTGTGGCAGCACGCCGTAGA

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[3]

est. P1 cotransduction: 59% [6]

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[3]

est. P1 cotransduction: 23% [6]
Synonyms:zjd-2231::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

NCBI (EcoliWiki Page)

GeneID:948625

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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 2.2 2.3 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 3.3 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 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
  6. ↑ 6.0 6.1 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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