yhdZ:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''yhdZ''  
''yhdZ''  
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!align=left {{table_heading_style}} |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
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''ECK3258, b3271, JW3239''<ref name='LIB:Riley_2006'/>
''ECK3258, b3271, JW3239''<ref name='LIB:Riley_2006'/>


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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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{{GBrowseFastaLink|ecoli|NC_000913|3420458|3421216|FASTA Dump}}
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*[http://biocyc.org/ECOLI/sequence?object=EG12837 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12837 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 3350328..3351086<br />{{GBrowseFigureByCoord|3350328|3351086|REL606|NC_012967}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3516687|3520477|FASTA Dump}}  
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[[REL606]]
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NC_012967: 3350328..3351086<br />{{GBrowseFigureByCoord|3350328|3351086|REL606|NC_012967}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Synonyms:zhb-3082::Tn10, zhd-3082::Tn10  
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10  


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Revision as of 02:24, 10 January 2010

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

Standard name

yhdZ

Mnemonic
Synonyms

ECK3258, b3271, JW3239[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

73.72 minutes 

MG1655: 3420458..3421216
gbrowse_img.php?coord=3420458..3421216&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3350328..3351086
gbrowse_img.php?coord=3350328..3351086&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3422291..3423049
gbrowse_img.php?coord=3422291..3423049&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3518203..3518961
gbrowse_img.php?coord=3518203..3518961&genome=ecoli_DH10B&name=DH10B&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

ΔyhdZ (Keio:JW3239)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW3239

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAGCCAAATTTTACTGCAACC

Primer 2:CCATGGATTACCTGCGATAAAAA

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[4]

est. P1 cotransduction: 83% [5]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[4]

est. P1 cotransduction: 76% [5]
Synonyms:zhb-3082::Tn10, zhd-3082::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:EG12837

EchoBASE (EcoliWiki Page)

EchoBASE:EB2686

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3271

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4037

EcoGene (EcoliWiki Page)

EcoGene:EG12837

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHDZ

ASAP (EcoliWikiPage)

ASAP:ABE-0010738


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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. ↑ 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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