yadI:Gene: Difference between revisions

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Revision as of 20:32, 17 August 2011

{{#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 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

yadI

Mnemonic

Systematic nomenclature

Synonyms

ECK0128, b0129, JW0125, agaX[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

3.12 minutes 

MG1655: 144577..145017
<gbrowseImage> name=NC_000913:144577..145017 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 147380..147820
<gbrowseImage> name=NC_012967:147380..147820 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 144576..145016
<gbrowseImage> name=NC_012759:144576..145016 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 144577..145017
<gbrowseImage> name=AC_000091:144577..145017 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 118681..119121
<gbrowseImage> name=NC_010473:118681..119121 source=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

ΔyadI (Keio:JW0125)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8402[3]

ΔyadI746::kan

PMID:16738554[2]

CGSC:103468


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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

JW0125

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTTAGGTTGGGTAATTACCTG

Primer 2:CCATACTCATACAAATTATGTTT

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[3]

est. P1 cotransduction: 4% [5]
Synonyms:zab-3051::Tn10 nnnThe start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 88% [5]

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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:EG12322

EchoBASE (EcoliWiki Page)

EchoBASE:EB2227

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0129

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0158

EcoGene (EcoliWiki Page)

EcoGene:EG12322

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YADI

ASAP (EcoliWikiPage)

ASAP:ABE-0000453


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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. ↑ 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).

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