ydfU:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ydfU

Mnemonic

Systematic nomenclature

Synonyms

ECK1554, b1560, JW5909[1], JW5909

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Notes

Location(s) and DNA Sequence

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<protect> 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

35.37 minutes 

MG1655: 1642328..1641279
<gbrowseImage> name=NC_000913:1641279..1642328 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1618721..1618143
<gbrowseImage> name=NC_012967:1618143..1618721 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1533338..1534285
<gbrowseImage> name=NC_012759:1533338..1534285 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1646018..1644969
<gbrowseImage> name=NC_007779:1644969..1646018 source=W3110 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

Strain DH10B

L209Q

Nonsynonomous mutation

PMID:18245285[2]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔydfU (Keio:JW5909)

deletion

deletion

PMID:16738554[3]

Shigen

Strain BW2952

A425T

PMID:19376874[4]

Relative to MG1655.

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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

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

22D11

Kohara Phage

Genobase

PMID:3038334[6]

12E2

Kohara Phage

Genobase

PMID:3038334[6]

7B6

Kohara Phage

Genobase

PMID:3038334[6]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[7]

est. P1 cotransduction: % [8]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[7]

est. P1 cotransduction: % [8]
Synonyms:zdh-925::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:G6831

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13833

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003420

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946108

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3594

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005209

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. Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  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. Ferenci, T et al. (2009) Genomic sequencing reveals regulatory mutations and recombinational events in the widely used MC4100 lineage of Escherichia coli K-12. J. Bacteriol. 191 4025-9 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 6.2 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
  7. 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. 8.0 8.1 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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