speC:Gene: Difference between revisions

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''ECK2960, b2965, JW5482''<ref name='LIB:Riley_2006'/>
''ECK2960, b2965, JW5482''<ref name='LIB:Riley_2006'/>
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3105676..3107811&plugin_action=Go FASTA Dump]  
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3105676..3107811&plugin_action=Go FASTA Dump]  
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!Feature type!!Location!!Description
!Feature type!!Location!!Description
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est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 13% <ref name='LIB:Nichols_linked_Tn'/>  
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Revision as of 08:36, 30 April 2008

{{#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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Standard name

speC

Mnemonic
Synonyms

ECK2960, b2965, JW5482[1]

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

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Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

66.92 minutes 

MG1655: 3107177..3105042
gbrowse_img.php?coord=3104042..3108177&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3107811..3105676
gbrowse_img.php?coord=3104676..3108811&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

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Feature type Location Description
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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔspeC (Keio:JW5482)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11419[3]

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

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Resource Resource Type Source Notes/Reference

JW5482

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAATCAATGAATATTGCCGC

Primer 2:CCtTTCAACACATAACCGTACAA

nupG511::Tn10

Linked marker

CAG18472 = CGSC7433[3]

est. P1 cotransduction: 96% [5]

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[3]

est. P1 cotransduction: 13% [5]

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:EG10961

EchoBASE (EcoliWiki Page)

EchoBASE:EB0954

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2965

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3553

EcoGene (EcoliWiki Page)

EcoGene:EG10961

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:SPEC

CGSC (EcoliWiki Page)

CGSC:159

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Notes

Links

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Name URL Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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. ↑ 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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