yafY: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
|
||
''yafY''  
''yafY''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0253, b0251, JW0240''<ref name='LIB:Riley_2006'/>, JW0240''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11083.S46a9abd075a76&page=11083&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0253, b0251, JW0240''<ref name='LIB:Riley_2006'/>
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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="W46a9abd106bf1"  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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5.72 minutes&nbsp;
5.72 minutes&nbsp;
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MG1655: 266191..265334<br />{{GBrowseFigureByCoord|264334|267191|ecoli|MG1655}}
MG1655: 266191..265334<br /><gbrowseImage>
name=NC_000913:265334..266191
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6126 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6126 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:264334..267191 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|264334|267191|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:265334..266191&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|265334|266191|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6126 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6126 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 265333..265776<br /><gbrowseImage>
name=NC_012759:265333..265776
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|265333|265776|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|265333|265776|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 266191..265334<br />{{GBrowseFigureByCoord|264334|267191|ecoli_W3110|W3110}}
W3110: 266191..265334<br /><gbrowseImage>
name=NC_007779:265334..266191
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:264334..267191 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|264334|267191|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:265334..266191&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|265334|266191|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 239881..239438<br /><gbrowseImage>
name=NC_010473:239438..239881
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|238552|240767|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|238552|240767|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="L46a9abd1a4b8f"  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====
====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="B46a9abd1e7e34"  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;yafY (Keio:JW0240)
''yafY(del)'' (Keio:JW0240)
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deletion
deletion
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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]
|
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0000853 yafY::Tn5KAN-I-SceI] (FB20102)
|
Insertion at nt 503 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20102]
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]  
contains [[pKD46]]  
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===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="Q4e04c5fc2bc51"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9abd2917ab"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW0240
JW0240
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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:CCTTCCTGATTGTCAGGGTTCGA  
Primer 2:CCTTCCTGATTGTCAGGGTTCGA  
|-
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[[:Category:Kohara_Phage:8G4|8G4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=128 Genobase]
|
PMID:3038334
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[[proA:Gene|proA81::Tn10]]
[[proA:Gene|proA81::Tn10]]
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est. P1 cotransduction: 83% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 83% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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[[lacI:Gene|lacI3042::Tn10]]
[[lacI:Gene|lacI3042::Tn10]]
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CAG18439 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39002 CGSC7334]<ref name='LIB:cgsc'/>
CAG18439 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39002 CGSC7334]<ref name='LIB:cgsc'/>
|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).


Synonyms:lacI42::Tn10
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CAG18439 also carries lacZ118(0c) (CGSC).
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:G6126
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EcoGene]]
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EcoGene:EG13337
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6126 EcoCyc:G6126]
[http://www.ncbi.nlm.nih.gov/gene?term=944934 GeneID:944934]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3121 EchoBASE:EB3121] 
RegulonDB:ECK120002746
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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]])
[[EchoBASE]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0251 EcoliGenExpDB:b0251] 
EchoBASE:EB3121
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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]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13337 EcoGene:EG13337] 
ASAP:ABE-0000853
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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:Gene List:CP4-6 prophage]]
[[Category:yaf genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:27, 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

yafY

Mnemonic

Systematic nomenclature

Synonyms

ECK0253, b0251, JW0240[1], JW0240

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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

5.72 minutes 

MG1655: 266191..265334
<gbrowseImage> name=NC_000913:265334..266191 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 265333..265776
<gbrowseImage> name=NC_012759:265333..265776 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 266191..265334
<gbrowseImage> name=NC_007779:265334..266191 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 239881..239438
<gbrowseImage> name=NC_010473:239438..239881 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

yafY(del) (Keio:JW0240)

deletion

deletion

PMID:16738554[2]

Shigen

yafY::Tn5KAN-I-SceI (FB20102)

Insertion at nt 503 in Plus orientation

PMID:15262929[3]

E. coli Genome Project:FB20102

contains pKD46

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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

JW0240

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACACAGGCAGAACGCCGCCA

Primer 2:CCTTCCTGATTGTCAGGGTTCGA

8G4

Kohara Phage

Genobase

PMID:3038334[5]

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[6]

est. P1 cotransduction: 83% [7]

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[6]

est. P1 cotransduction: % [7]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:G6126

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13337

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944934

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002746

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3121

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000853

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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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).

Categories

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