yaaW: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="I46a9a66052933"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yaaW''  
''yaaW''  
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK0011, b0011, JW0010, htpY''<ref name='LIB:Riley_2006'/>
''ECK0011, b0011, JW0010, htpY''<ref name='LIB:Riley_2006'/>, htgA, htpY''
|-
 
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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="J46a9a660cad68"  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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6082 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6082 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:9643..12356 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|9643|12356|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:10643..11356&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|10643|11356|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6082 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6082 EcoCyc Sequence Dump]  
|-
|-
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[[BW2952]]
|
 
|
NC_012759: 10643..11356<br />{{GBrowseFigureByCoord|10643|11356|BW2952|NC_012759}}
|
{{GBrowseLink|BW2952|012759|10643|NC_11356|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|10643|NC_11356|FASTA Dump}}
|-  
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W3110
W3110
|
|
&nbsp;
 
|
W3110: 11356..10643<br />{{GBrowseFigureByCoord|9643|12356|W3110|W3110}}
|
{{GBrowseLink|W3110|NC_007779|9643|12356|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|10643|11356|FASTA Dump}}
|-
|
[[DH10B]]
|
 
|
|
W3110: 11356..10643<br />{{GBrowseFigureByCoord|9643|12356|ecoli_W3110|W3110}}  
DH10B: 11356..10643<br />{{GBrowseFigureByCoord|9217|12782|DH10B|DH10B}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:9643..12356 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|9217|12782|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:10643..11356&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|9217|12782|FASTA Dump}}
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===Notes===
===Notes===
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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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|- {{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;yaaW (Keio:JW0010)
''yaaW(del)'' (Keio:JW0010)
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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]
[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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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW0010
JW0010
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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:CCGACCTGAGTGGCGCTAACCAT  
Primer 2:CCGACCTGAGTGGCGCTAACCAT  
|-
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[[:Category:Kohara_Phage:9E4|9E4]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=101 Genobase]
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PMID:3038334
|-
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[[:Category:Kohara_Phage:9E4|9E4]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=101 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6H3|6H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=102 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6H3|6H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=102 Genobase]
|
PMID:3038334
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[[thrA:Gene|thrA34::Tn10]]
[[thrA:Gene|thrA34::Tn10]]
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CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
CAG18442 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38985 CGSC7320]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 69% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:thr-34::Tn10  
Synonyms:thr-34::Tn10  
|-
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|
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[[carB:Gene|carB96::Tn10]]
[[carB:Gene|carB96::Tn10]]
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CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
CAG12093 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38008 CGSC7322]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:car-96::Tn10


Synonyms:car-96::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=G6082 EcoCyc:G6082]
EcoCyc:G6082
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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]])
[[EchoBASE]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4086 EchoBASE:EB4086]
EchoBASE:EB4086
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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]])
[[EcoGene]]
|
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[http://ecogene.org/geneinfo.php?eg_id=EG14340 EcoGene:EG14340]
EcoGene:EG14340
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
ASAP:ABE-0000037
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0000037&formSubmitReturn=1 ASAP:ABE-0000037] 
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6082 ECOCYC:G6082]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=944771 GeneID:944771]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[RegulonDB]]
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RegulonDB:ECK120002702
|
''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:yaa genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:36, 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

yaaW

Mnemonic
Synonyms

ECK0011, b0011, JW0010, htpY[1], htgA, htpY

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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

0.23 minutes 

MG1655: 11356..10643
gbrowse_img.php?coord=9643..12356&genome=ecoli&name=MG1655&trackset=0&width=300&.png

BW2952

NC_012759: 10643..11356
gbrowse_img.php?coord=10643..11356&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 11356..10643
gbrowse_img.php?coord=9643..12356&genome=W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 11356..10643
gbrowse_img.php?coord=9217..12782&genome=DH10B&name=DH10B&trackset=0&width=300&.png

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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

yaaW(del) (Keio:JW0010)

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

JW0010

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAATGTTAATTACCTGAATGA

Primer 2:CCGACCTGAGTGGCGCTAACCAT

9E4

Kohara Phage

Genobase

PMID:3038334[4]

9E4

Kohara Phage

Genobase

PMID:3038334[4]

6H3

Kohara Phage

Genobase

PMID:3038334[4]

6H3

Kohara Phage

Genobase

PMID:3038334[4]

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[5]

est. P1 cotransduction: 69% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[5]

est. P1 cotransduction: 45% [6]
Synonyms:car-96::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:G6082

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4086

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0011

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0016

EcoGene

EcoGene:EG14340

Escherichia coli str. K-12 substr. MG1655

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z0011

ASAP

ASAP:ABE-0000037

Escherichia coli str. K-12 substr. MG1655

EcoCyc (EcoliWiki Page)

ECOCYC:G6082

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944771

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002702

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 4.2 4.3 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).

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