tfaD:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 17:08, 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

tfaD

Mnemonic
Synonyms

ECK0553, b0561, JW5815, yicF, ybcX, ylcF[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

12.52 minutes 

MG1655: 580757..581320
<gbrowseImage> name=NC_000913:580757..581320 source=ecoli preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 580757..581320
<gbrowseImage> name=AC_000091:580757..581320 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 520215..520652
<gbrowseImage> name=NC_010473:520215..520652 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 633475..633912
<gbrowseImage> name=NC_010473:633475..633912 source=ecoli_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

ΔtfaD (Keio:JW5815)

deletion

deletion

PMID:16738554[3]

Shigen


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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

JW5815

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAATGCGATGGGCAGCGACTA

Primer 2:CCtTCCCTGACAGGGTTCGTAGG

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[5]

est. P1 cotransduction: 33% [6]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[5]

est. P1 cotransduction: 7% [6]
Synonyms:zbd-601::Tn10, zbe-601::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:G6315

EchoBASE (EcoliWiki Page)

EchoBASE:EB3404

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0561

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3173

EcoGene (EcoliWiki Page)

EcoGene:EG13640

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z2983


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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. ↑ 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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