potF: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="W46a9ba30863e7"  class=" tableEdit Gene_nomenclature_table" 
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!{{table_heading_style}} |Standard name
|
''potF''
|-
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Standard name
|
||
Putrescine-ornithine transporter<ref name='LIB:EcoGene'/>
''potF''
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Mnemonic
|
||
''ECK0845, b0854, JW0838''<ref name='LIB:Riley_2006'/>
Putrescine-ornithine transporter
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!align=left {{table_heading_style}} |Synonyms
||
''ECK0845, b0854, JW0838''<ref name='LIB:Riley_2006'/>, JW0838''
 
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===Notes===
===Notes===
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<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="U46a9ba310a5b9"  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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19.25 minutes&nbsp;
19.25 minutes&nbsp;
|
|
MG1655: 893007..894119<br />{{GBrowseFigureByCoord|892007|895119|ecoli|MG1655}}
MG1655: 893007..894119<br /><gbrowseImage>
name=NC_000913:893007..894119
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11629 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11629 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:892007..895119 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|892007|895119|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:893007..894119&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|893007|894119|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11629 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11629 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 910491..911603<br /><gbrowseImage>
name=NC_012967:910491..911603
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|910491|911603|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|910491|911603|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 795975..797087<br /><gbrowseImage>
name=NC_012759:795975..797087
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|795975|797087|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|795975|797087|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 894206..895318<br />{{GBrowseFigureByCoord|893206|896318|ecoli_W3110|W3110}}  
W3110: 894206..895318<br /><gbrowseImage>
name=NC_007779:894206..895318
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|893206|896318|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|894206|895318|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 946935..948047<br /><gbrowseImage>
name=NC_010473:946935..948047
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:893206..896318 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|944711|950271|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:894206..895318&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|944711|950271|FASTA Dump}}
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===Notes===
===Notes===
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{{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="L46a9ba31a814c"  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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Coding Start (SO:0000323)
|
[[MG1655]]
|
893085
|
Edman degradation
|
PMID:8416922<br />PMID:9298646<br />
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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="S46a9ba31e83af"  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;potF (Keio:JW0838)
&Delta;potF (Keio:JW0838)
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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=107156 CGSC8875]<ref name='LIB:cgsc'/>
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''&#916;potF755::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102408|CGSC:102408]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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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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JW0838
JW0838
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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:CCTTTTCCGCTCTTCACTTTGGT  
Primer 2:CCTTTTCCGCTCTTCACTTTGGT  
|-
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[[:Category:Kohara_Phage:5F4|5F4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=210 Genobase]
|
PMID:3038334
|-  
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zbh-29::Tn10
zbh-29::Tn10
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CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zbi-29::Tn10  
Synonyms:zbi-29::Tn10  
|-
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zca-1230::Tn10
zca-1230::Tn10
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CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 8% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::Tn10


Synonyms:zbj-1230::Tn10
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11629 EcoCyc:EG11629] 
|
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[[EcoCyc]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
EcoCyc:EG11629
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1586 EchoBASE:EB1586]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
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[[EcoGene]]
|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
EcoGene:EG11629
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0854 EcoliGenExpDB:b0854]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|
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|-
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0987 ECOL199310CYC:C0987] 
RegulonDB:ECK120001577
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://ecogene.org/geneinfo.php?eg_id=EG11629 EcoGene:EG11629]
[http://www.ncbi.nlm.nih.gov/gene?term=945480 GeneID:945480]
|
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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=POTF ECOO157CYC:POTF] 
EchoBASE:EB1586
|
|
''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/31694 CGSC:31694] 
ASAP:ABE-0002913
|
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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:pot 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

potF

Mnemonic

Putrescine-ornithine transporter

Synonyms

ECK0845, b0854, JW0838[1], JW0838

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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

19.25 minutes 

MG1655: 893007..894119
<gbrowseImage> name=NC_000913:893007..894119 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 910491..911603
<gbrowseImage> name=NC_012967:910491..911603 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 795975..797087
<gbrowseImage> name=NC_012759:795975..797087 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 894206..895318
<gbrowseImage> name=NC_007779:894206..895318 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 946935..948047
<gbrowseImage> name=NC_010473:946935..948047 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

Coding Start (SO:0000323)

MG1655

893085

Edman degradation

PMID:8416922[2]
PMID:9298646[3]


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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

ΔpotF (Keio:JW0838)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8875[5]

ΔpotF755::kan

PMID:16738554[4]

CGSC:102408


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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

JW0838

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCACCGCCTTAAATAAAAAATG

Primer 2:CCTTTTCCGCTCTTCACTTTGGT

5F4

Kohara Phage

Genobase

PMID:3038334[7]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[5]

est. P1 cotransduction: 1% [8]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 8% [8]
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:EG11629

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11629

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001577

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945480

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1586

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002913

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. ↑ Pistocchi, R et al. (1993) Characteristics of the operon for a putrescine transport system that maps at 19 minutes on the Escherichia coli chromosome. J. Biol. Chem. 268 146-52 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 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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