yffR: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:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="W46a9de425fedf"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yffR''  
''yffR''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||
 
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2444, b2449, unique to MG1655''<ref name='LIB:Riley_2006'/>
''ECK2444, b2449, unique to MG1655''<ref name='LIB:Riley_2006'/>
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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="F46a9de42dd8c7"  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
|-
|-  
|
|
MG1655
MG1655
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55.22 minutes&nbsp;
55.22 minutes&nbsp;
|
|
MG1655: 2562002..2562394<br />{{GBrowseFigureByCoord|2561002|2563394|ecoli|MG1655}}
MG1655: 2562002..2562394<br /><gbrowseImage>
name=NC_000913:2562002..2562394
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7279 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7279 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2561002..2563394 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2561002|2563394|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2562002..2562394&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2562002|2562394|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7279 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7279 EcoCyc Sequence Dump]  
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|
[[BW2952]]
|
 
|
NC_012759: 2447807..2448199<br /><gbrowseImage>
name=NC_012759:2447807..2448199
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2447807|2448199|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2447807|2448199|FASTA Dump}}
|-
|
[[DH10B]]
|
 
|
DH10B: 2653767..2654159<br /><gbrowseImage>
name=NC_010473:2653767..2654159
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2652983|2654943|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2652983|2654943|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="J46a9de4338f56"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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====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="G46a9de437e936"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
&Delta;yffR (Keio:)
|
deletion
|
deletion
|
 
|


|
|- class="tableEdit_footer"
[[PMID:16738554]]<ref name=PMID:16738554/>
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15463.G46a9de437e936&page=15463&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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:
Status:
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Primer 2:  
Primer 2:  
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[[nupC:Gene|nupC510::Tn10]]
[[nupC:Gene|nupC510::Tn10]]
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est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[purC:Gene|purC80::Tn10]]
[[purC:Gene|purC80::Tn10]]
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est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>  
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-
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[[EcoCyc]]
|
EcoCyc:G7279
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG14179
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7279 EcoCyc:G7279] 
RegulonDB:ECK120003853
|
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3931 EchoBASE:EB3931]
[http://www.ncbi.nlm.nih.gov/gene?term=946931 GeneID:946931]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2449 EcoliGenExpDB:b2449] 
EchoBASE:EB3931
|
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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]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG14179 EcoGene:EG14179] 
ASAP:ABE-0008074
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
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{{RefHelp}}
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<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Gene List:Eut/CPZ-55 prophage]]
[[Category:yff genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

yffR

Mnemonic

Systematic nomenclature

Synonyms

ECK2444, b2449, unique to MG1655[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

55.22 minutes 

MG1655: 2562002..2562394
<gbrowseImage> name=NC_000913:2562002..2562394 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2447807..2448199
<gbrowseImage> name=NC_012759:2447807..2448199 source=BW2952 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2653767..2654159
<gbrowseImage> name=NC_010473:2653767..2654159 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
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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

Plasmid clone

Shigen

PMID:16769691[2]

Status:

Primer 1:

Primer 2:

nupC510::Tn10

Linked marker

CAG18468 = CGSC7410[3]

est. P1 cotransduction: 9% [4]

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[3]

est. P1 cotransduction: 29% [4]

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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:G7279

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14179

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003853

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946931

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3931

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008074

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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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).

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