rayT:Gene: Difference between revisions

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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
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[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
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==Nomenclature==
==Nomenclature==
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!{{table_heading_style}} |Mnemonic
!{{table_heading_style}} |Mnemonic
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Systematic nomenclature<ref name='LIB:EcoGene'/>
 
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!{{table_heading_style}} |Synonyms
!{{table_heading_style}} |Synonyms
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''ECK0229, b0228, JW0218''<ref name='LIB:Riley_2006'/>
''ECK0229, b0228, JW0218''<ref name='LIB:Riley_2006'/>
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est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 66% <ref name='LIB:Nichols_linked_Tn'/>  
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__NOTOC__
__NOTOC__
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]

Revision as of 00:58, 2 August 2007

{{#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 Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

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Standard name

yafM

Mnemonic
Synonyms

ECK0229, b0228, JW0218[1]

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

Notes

Location(s) and DNA Sequence

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Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

5.34 minutes 

MG1655: 247637..248134
gbrowse_img.php?coord=246637..249134&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 247637..248134
gbrowse_img.php?coord=246637..249134&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

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Feature type Location Description
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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔyafM (Keio:JW0218)

deletion

deletion

PMID:16738554[2]

Shigen

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

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Resource Resource Type Source Notes/Reference

JW0218

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCTCTGAATATCGTCGTTATTA

Primer 2:CCTGAAATGATACGCTCCCCGGC

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[4]

est. P1 cotransduction: 57% [5]

Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[4]

est. P1 cotransduction: 66% [5]

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G6112

EchoBASE (EcoliWiki Page)

EchoBASE:EB2944

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0228

EcoGene (EcoliWiki Page)

EcoGene:EG13150

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAFM

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Notes

Links

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Name URL Comments
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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. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  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).


Categories

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