tfaD:Gene: Difference between revisions

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W3110: 580757..581320<br /><gbrowseImage>
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{{GBrowseLink|W3110|AC_000091|579757|582320|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|580757|581320|FASTA Dump}}  
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.ncbi.nlm.nih.gov/gene?term=945171 GeneID:945171]
RegulonDB:ECK120002923
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[RegulonDB]]
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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RegulonDB:ECK120002923
[http://www.ncbi.nlm.nih.gov/gene?term=945171 GeneID:945171]
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
Escherichia coli str. K-12 substr. MG1655  
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Latest revision as of 20:33, 19 September 2013

{{#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

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=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 580757..581320
<gbrowseImage> name=NC_007779:580757..581320 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

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

DH10B

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

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

23E10

Kohara Phage

Genobase

PMID:3038334[5]

12A1

Kohara Phage

Genobase

PMID:3038334[5]

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[6]

est. P1 cotransduction: 33% [7]
Synonyms:purE79::Tn10

dsbG601::Tn10

Linked marker

CAG12149 = CGSC7346[6]

est. P1 cotransduction: 7% [7]
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

EcoCyc:G6315

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13640

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002923

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945171

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3404

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0001917

Escherichia coli str. K-12 substr. MG1655

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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 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 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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