araE:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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Revision as of 22:36, 24 June 2011

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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

araE

Mnemonic

Arabinose

Synonyms

ECK2839, b2841, JW2809[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

64.2 minutes 

MG1655: 2980204..2978786
<gbrowseImage> name=NC_000913:2978786..2980204 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2876803..2875385
<gbrowseImage> name=NC_012967:2875385..2876803 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2865934..2867352
<gbrowseImage> name=NC_012759:2865934..2867352 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2980838..2979420
<gbrowseImage> name=AC_000091:2979420..2980838 source=MG1655_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3074074..3072656
<gbrowseImage> name=NC_010473:3072656..3074074 source=MG1655_DH10B preset=GeneLocation </gbrowseImage>

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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

ΔaraE (Keio:JW2809)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10196[3]

araE::Tn5KAN-I-SceI (FB20957)

Insertion at nt 940 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20957

does not contain pKD46

araE::Tn5KAN-I-SceI (FB20958)

Insertion at nt 940 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20958

contains pKD46

araE452

CGSC:80477

araE455

CGSC:80479

araE79

CGSC:80486

ΔaraE766::kan

PMID:16738554[2]

CGSC:100024


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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

JW2809

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGTTACTATCAATACGGAATC

Primer 2:CCGACGCCGATATTTCTCAACTT

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 34% [6]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: % [6]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10056

EchoBASE (EcoliWiki Page)

EchoBASE:EB0054

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2841

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3438

EcoGene (EcoliWiki Page)

EcoGene:EG10056

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ARAE

CGSC (EcoliWiki Page)

CGSC:1024

ASAP (EcoliWikiPage)

ASAP:ABE-0009319


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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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 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
  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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