yigA:Gene: Difference between revisions

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!align=left |Standard name
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''yigA''  
''yigA''
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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Systematic nomenclature
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>
''ECK3805, b3810, JW3783''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yig genes]][[Category:Gene_List:REL606]]
[[Category:yig genes]][[Category:Gene_List:REL606]]
[[Category:y genes]]

Revision as of 22:14, 25 February 2010

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

Standard name

yigA

Mnemonic

Systematic nomenclature

Synonyms

ECK3805, b3810, JW3783[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

86.08 minutes 

MG1655: 3993606..3994313
gbrowse_img.php?coord=3993606..3994313&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3957420..3958127
gbrowse_img.php?coord=3957420..3958127&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3641098..3640391
gbrowse_img.php?coord=3640391..3641098&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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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 Location Description
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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

L156STOP

Nonsense mutation

PMID:18245285[2]

ASAP

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

ΔyigA (Keio:JW3783)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10750[4]

ΔyigA756::kan

PMID:16738554[3]

CGSC:105376


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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

JW3783

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAGCAACCAGGGGAAGAACT

Primer 2:CCTACGCGTTCAATCCAACGCTC

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[4]

est. P1 cotransduction: 18% [6]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[4]

est. P1 cotransduction: 59% [6]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG11201

EchoBASE (EcoliWiki Page)

EchoBASE:EB1186

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3810

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4731

EcoGene (EcoliWiki Page)

EcoGene:EG11201

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YIGA

ASAP (EcoliWikiPage)

ASAP:ABE-0012444


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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. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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 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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