allR:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''allR''  
''allR''  
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!align=left {{table_heading_style}} |Mnemonic
!align=left |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
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''ECK0499, b0506, JW0494, gclR, glxA3, ybbU''<ref name='LIB:Riley_2006'/>
''ECK0499, b0506, JW0494, gclR, glxA3, ybbU''<ref name='LIB:Riley_2006'/>


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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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{{GBrowseFastaLink|ecoli|NC_000913|532235|533050|FASTA Dump}}
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*[http://biocyc.org/ECOLI/sequence?object=G6276 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6276 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 505177..505992<br />{{GBrowseFigureByCoord|505177|505992|REL606|NC_012967}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|469936|474011|FASTA Dump}}  
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[[REL606]]
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NC_012967: 505177..505992<br />{{GBrowseFigureByCoord|505177|505992|REL606|NC_012967}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Synonyms:purE79::Tn10  
Synonyms:purE79::Tn10  


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Revision as of 23:58, 8 January 2010

{{#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

allR

Mnemonic
Synonyms

ECK0499, b0506, JW0494, gclR, glxA3, ybbU[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

11.47 minutes 

MG1655: 532235..533050
gbrowse_img.php?coord=532235..533050&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 505177..505992
gbrowse_img.php?coord=505177..505992&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 532235..533050
gbrowse_img.php?coord=532235..533050&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 471566..472381
gbrowse_img.php?coord=471566..472381&genome=ecoli_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 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

ΔallR (Keio:JW0494)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8639[3]

ΔallR789::kan

PMID:16738554[2]

CGSC:99978


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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

JW0494

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACGGAAGTTAGACGGCGCGG

Primer 2:CCTGGATGTGCTTTCAGTCCCAA

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 29% [5]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 49% [5]
Synonyms:purE79::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 (EcoliWiki Page)

EcoCyc:G6276

EchoBASE (EcoliWiki Page)

EchoBASE:EB3382

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0506

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0621

EcoGene (EcoliWiki Page)

EcoGene:EG13616

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBBU

ASAP (EcoliWikiPage)

ASAP:ABE-0001750


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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. ↑ 2.0 2.1 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. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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. ↑ 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).

Categories

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