nikR:Gene: Difference between revisions

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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''nikR''  
''nikR''  
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>
''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>
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===Notes===
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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{{GBrowseFastaLink|ecoli|NC_000913|3616611|3617012|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|3616611|3617012|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11519 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11519 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|4021426|4021827|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|4021426|4021827|FASTA Dump}}  
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===Notes===
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====Notes====
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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;nikR (Keio:JW3446)
&Delta;nikR (Keio:JW3446)
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|[[PMID:16738554]]<ref name=PMID:16738554/>
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[[PMID:16738554]]<ref name=PMID:16738554/>
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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JW3446
JW3446
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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]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
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Primer 2:CCATCTTCCTTCGGCAAGCACTG  
Primer 2:CCATCTTCCTTCGGCAAGCACTG  
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zhg-50::Tn10
zhg-50::Tn10
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CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zhf-50::Tn10, zhf-5::Tn10  
 
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zic-4901::Tn10
zic-4901::Tn10
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011366&formSubmitReturn=1 ASAP:ABE-0011366]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0011366&formSubmitReturn=1 ASAP:ABE-0011366]
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:32, 21 January 2009

{{#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 Alleles and Phenotypes 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

nikR

Mnemonic
Synonyms

ECK3465, b3481, JW3446, yhhG[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

77.95 minutes 

MG1655: 3616611..3617012
gbrowse_img.php?coord=3615611..3618012&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 4021827..4021426
gbrowse_img.php?coord=4020426..4022827&genome=ecoli_W3110&name=W3110&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 Location Description
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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

ΔnikR (Keio:JW3446)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW3446

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCCAACGAGTCACCATCACGCT

Primer 2:CCATCTTCCTTCGGCAAGCACTG

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 38% [5]nnSynonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: % [5]

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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 (EcoliWiki Page)

EcoCyc:EG11519

EchoBASE (EcoliWiki Page)

EchoBASE:EB1481

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3481

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4274

EcoGene (EcoliWiki Page)

EcoGene:EG11519

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHHG

ASAP (EcoliWikiPage)

ASAP:ABE-0011366


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Notes

Links

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Name URL Comments
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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. ↑ 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 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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