yzfA: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="I46aa0a5236d63"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yzfA''  
''yzfA''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4219, b4223, JW4182, yjfA, ileR''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK4219, b4223, JW4182, yjfA, ileR''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='150244'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46aa0a52bacd4"  class=" tableEdit Gene_location_table" 
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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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95.83 minutes&nbsp;
95.83 minutes&nbsp;
|
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MG1655: 4446268..4445999<br />{{GBrowseFigureByCoord|4444999|4447268|ecoli|MG1655}}
MG1655: 4446268..4445999<br /><gbrowseImage>
name=NC_000913:4445999..4446268
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11213 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11213 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4444999|4447268|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4444999|4447268|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4445999..4446268&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4445999|4446268|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11213 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11213 EcoCyc Sequence Dump]  
|-
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 4452925..4452656<br />{{GBrowseFigureByCoord|4451656|4453925|ecoli_W3110|W3110}}  
W3110: 4452925..4452656<br /><gbrowseImage>
name=NC_007779:4452656..4452925
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4451656|4453925|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4452656|4452925|FASTA Dump}}  
|-
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[[DH10B]]
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4451656..4453925 GBrowse(W3110)]
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4452656..4452925&plugin_action=Go FASTA Dump]
DH10B: 4546630..4546361<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:4546361..4546630
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|4545823|4547168|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|4545823|4547168|FASTA Dump}}
 
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===Notes===
===Notes===
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====Notes====
====Notes====
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{|class = 'sortable' {{Prettytable}} id='150246'
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|- {{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;yzfA (Keio:JW4182)
&Delta;yzfA (Keio:JW4182)
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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]
|
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<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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JW4182
JW4182
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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:CCGTATCGATAACTACCAGTTGT  
Primer 2:CCGTATCGATAACTACCAGTTGT  
|-
|-
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[[:Category:Kohara_Phage:E1H3|E1H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=657 Genobase]
|
PMID:3038334
|-  
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[[ytfN:Gene|zjf-920::Tn10]]
[[ytfN:Gene|zjf-920::Tn10]]
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CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
CAG12019 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40608 CGSC7484]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 96% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 96% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zjh-901::Tn10, zjg-920::Tn10  
Synonyms:zjh-901::Tn10, zjg-920::Tn10  
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[[mdoB:Gene|mdoB202::Tn10]]
[[mdoB:Gene|mdoB202::Tn10]]
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CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
CAG18430 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40618 CGSC7488]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zjj-202::Tn10, zji-202::Tn10


Synonyms:zjj-202::Tn10, zji-202::Tn10
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===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=EG11213 EcoCyc:EG11213] 
EcoCyc:EG11213
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4373 EchoBASE:EB4373] 
EcoGene:EG11213
|
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''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]]
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b4223 EcoliGenExpDB:b4223] 
RegulonDB:ECK120001193
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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]])
[[EchoBASE]]
|
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[http://ecogene.org/geneinfo.php?eg_id=EG11213 EcoGene:EG11213] 
EchoBASE:EB4373
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
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[http://BioCyc.org/ECOO157/new-image?object=YJFA ECOO157CYC:YJFA] 
ASAP:ABE-0013816
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[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:yzf genes]]
[[Category:yzf genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:52, 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

yzfA

Mnemonic
Synonyms

ECK4219, b4223, JW4182, yjfA, ileR[1][2]

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Notes

Location(s) and DNA Sequence

[back to top]


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

95.83 minutes 

MG1655: 4446268..4445999
<gbrowseImage> name=NC_000913:4445999..4446268 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4452925..4452656
<gbrowseImage> name=NC_007779:4452656..4452925 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4546630..4546361
<gbrowseImage> name=NC_010473:4546361..4546630 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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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔyzfA (Keio:JW4182)

deletion

deletion

PMID:16738554[3]

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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Resource Resource Type Source Notes/Reference

JW4182

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCATATGGTTACTTATCCCTG

Primer 2:CCGTATCGATAACTACCAGTTGT

E1H3

Kohara Phage

Genobase

PMID:3038334[5]

zjf-920::Tn10

Linked marker

CAG12019 = CGSC7484[6]

est. P1 cotransduction: 96% [7]
Synonyms:zjh-901::Tn10, zjg-920::Tn10

mdoB202::Tn10

Linked marker

CAG18430 = CGSC7488[6]

est. P1 cotransduction: % [7]
Synonyms:zjj-202::Tn10, zji-202::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:EG11213

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11213

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001193

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4373

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013816

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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
  4. ↑ 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. ↑ 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 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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