yafY: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 23:37, 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

yafY

Mnemonic

Systematic nomenclature

Synonyms

ECK0253, b0251, JW0240[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

5.72 minutes 

MG1655: 266191..265334
gbrowse_img.php?coord=265334..266191&genome=ecoli&name=MG1655&trackset=0&width=300&.png

BW2952

NC_012759: 265333..265776
gbrowse_img.php?coord=265333..265776&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 266191..265334
gbrowse_img.php?coord=265334..266191&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 239881..239438
gbrowse_img.php?coord=239438..239881&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

ΔyafY (Keio:JW0240)

deletion

deletion

PMID:16738554[2]

Shigen

yafY::Tn5KAN

PMID:12519969[3]

ASAP

At position 503 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20102

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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

JW0240

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACACAGGCAGAACGCCGCCA

Primer 2:CCTTCCTGATTGTCAGGGTTCGA

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[5]

est. P1 cotransduction: 83% [6]

lacI3042::Tn10

Linked marker

CAG18439 = CGSC7334[5]

est. P1 cotransduction: % [6]
Synonyms:lacI42::Tn10 nnnCAG18439 also carries lacZ118(0c) (CGSC).

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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:G6126

EchoBASE (EcoliWiki Page)

EchoBASE:EB3121

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0251

EcoGene (EcoliWiki Page)

EcoGene:EG13337

ASAP (EcoliWikiPage)

ASAP:ABE-0000853


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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. ↑ 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. ↑ Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 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).

Categories

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