acrE:Gene: Difference between revisions

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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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Revision as of 22:15, 10 May 2010

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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

acrE

Mnemonic

Acridine

Synonyms

ECK3252, b3265, JW3233, G7979[1][2]

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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

73.54 minutes 

MG1655: 3411886..3413043
gbrowse_img.php?coord=3411886..3413043&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3341755..3342912
gbrowse_img.php?coord=3341755..3342912&genome=REL606&name=NC_012967&trackset=0&width=300&.png

BW2952

NC_012759: 3299034..3300191
gbrowse_img.php?coord=3299034..3300191&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 3413719..3414876
gbrowse_img.php?coord=3413719..3414876&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3509631..3510788
gbrowse_img.php?coord=3509631..3510788&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 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

ΔacrE (Keio:JW3233)

deletion

deletion

PMID:16738554[3]

Shigen

acrE::Tn5KAN

PMID:12519969[4]

ASAP

At position 611 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB21091

acrE::Tn5KAN

PMID:12519969[4]

ASAP

At position 611 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB21092

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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

JW3233

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCACGAAACATGCCAGGTTTTT

Primer 2:CCtTTCGATGCAGTATCTGCGGG

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[6]

est. P1 cotransduction: 11% [7]
Synonyms:zha-6::Tn10

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[6]

est. P1 cotransduction: 91% [7]
Synonyms:zhd-3083::Tn10, zhe-3083::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:EG10266

EchoBASE (EcoliWiki Page)

EchoBASE:EB0262

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3265

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4031

EcoGene (EcoliWiki Page)

EcoGene:EG10266

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ACRE

CGSC (EcoliWiki Page)

CGSC:813

ASAP (EcoliWikiPage)

ASAP:ABE-0010722


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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. ↑ 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. ↑ 4.0 4.1 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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