epd:Gene: Difference between revisions

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''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3071328..3072347&plugin_action=Go FASTA Dump]  
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3071328..3072347&plugin_action=Go FASTA Dump]  
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!Feature type!!Location!!Description
!Feature type!!Location!!Description
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Synonyms:zgd-210::Tn10, zgf-210::Tn10  
Synonyms:zgd-210::Tn10, zgf-210::Tn10  
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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

epd

Mnemonic
Synonyms

ECK2923, b2927, JW2894, gapB, gap2[1][2]

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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

66.18 minutes 

MG1655: 3071713..3070694
gbrowse_img.php?coord=3069694..3072713&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3072347..3071328
gbrowse_img.php?coord=3070328..3073347&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

Δepd (Keio:JW2894)

deletion

deletion

PMID:16738554[3]

Shigen

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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

JW2894

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACCGTACGCGTAGCGATAAA

Primer 2:CCtCTGAAAGCAACAGTAGCCAT

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[5]

est. P1 cotransduction: % [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[5]

est. P1 cotransduction: 60% [6]

Synonyms:zgd-210::Tn10, zgf-210::Tn10

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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:EG10368

EchoBASE (EcoliWiki Page)

EchoBASE:EB0363

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2927

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3505

EcoGene (EcoliWiki Page)

EcoGene:EG10368

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:EPD

CGSC (EcoliWiki Page)

CGSC:32089

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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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
  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 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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