yphC: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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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yphC''  
''yphC''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2542, b2545, JW5842''<ref name='LIB:Riley_2006'/>, JW5842''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15659.W46a9e08e4226f&page=15659&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2542, b2545, JW5842''<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="E46a9e08ebfd23"  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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57.61 minutes&nbsp;
57.61 minutes&nbsp;
|
|
MG1655: 2673783..2672722<br />{{GBrowseFigureByCoord|2671722|2674783|ecoli|MG1655}}
MG1655: 2673783..2672722<br /><gbrowseImage>
name=NC_000913:2672722..2673783
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7339 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7339 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2671722..2674783 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2671722|2674783|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2672722..2673783&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2672722|2673783|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7339 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7339 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2596460..2595399<br /><gbrowseImage>
name=NC_012967:2595399..2596460
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2595399|2596460|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2595399|2596460|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2558527..2559588<br /><gbrowseImage>
name=NC_012759:2558527..2559588
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2558527|2559588|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2558527|2559588|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2674417..2673356<br />{{GBrowseFigureByCoord|2672356|2675417|ecoli_W3110|W3110}}
W3110: 2674417..2673356<br /><gbrowseImage>
name=NC_007779:2673356..2674417
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2672356..2675417 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2672356|2675417|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2673356..2674417&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2673356|2674417|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2765548..2764487<br /><gbrowseImage>
name=NC_010473:2764487..2765548
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2762365|2767670|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2762365|2767670|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="E46a9e08f790cd"  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====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9e08fbf530"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;yphC (Keio:JW5842)
&Delta;yphC (Keio:JW5842)
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==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="F4e04cca121366"  class=" tableEdit Genetic_interaction_table dataTable" 
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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
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JW5842
JW5842
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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:Clone OK
Status:Clone OK
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Primer 2:CCATCCGGGAAGTTAATCACAAC  
Primer 2:CCATCCGGGAAGTTAATCACAAC  
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[[:Category:Kohara_Phage:6F10|6F10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=431 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:8E12|8E12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=432 Genobase]
|
PMID:3038334
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|
[[hcaT:Gene|zfh-208::Tn10]]
|
Linked marker
|
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 72% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zff-208::Tn10
|-
|
[[nadB:Gene|nadB51::Tn10]]
|
Linked marker
|
CAG18480 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40090 CGSC7419]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 22% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7339 EcoCyc:G7339] 
EcoCyc:G7339
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3237 EchoBASE:EB3237] 
EcoGene:EG13464
|
|
''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]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2545 EcoliGenExpDB:b2545] 
RegulonDB:ECK120003909
|
|
''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]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3067 ECOL199310CYC:C3067]
[http://www.ncbi.nlm.nih.gov/gene?term=947019 GeneID:947019]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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|
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13464 EcoGene:EG13464] 
EchoBASE:EB3237
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YPHC_2 ECOO157CYC:YPHC_2] 
ASAP:ABE-0008370
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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:yph genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

yphC

Mnemonic

Systematic nomenclature

Synonyms

ECK2542, b2545, JW5842[1], JW5842

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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

57.61 minutes 

MG1655: 2673783..2672722
<gbrowseImage> name=NC_000913:2672722..2673783 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2596460..2595399
<gbrowseImage> name=NC_012967:2595399..2596460 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2558527..2559588
<gbrowseImage> name=NC_012759:2558527..2559588 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2674417..2673356
<gbrowseImage> name=NC_007779:2673356..2674417 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2765548..2764487
<gbrowseImage> name=NC_010473:2764487..2765548 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

ΔyphC (Keio:JW5842)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW5842

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAAAACGATGCTGGCAGCTTA

Primer 2:CCATCCGGGAAGTTAATCACAAC

6F10

Kohara Phage

Genobase

PMID:3038334[4]

8E12

Kohara Phage

Genobase

PMID:3038334[4]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 72% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[5]

est. P1 cotransduction: 22% [6]

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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:G7339

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13464

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003909

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947019

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3237

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008370

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. ↑ 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. ↑ 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
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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