parE:Gene: Difference between revisions

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Update TableEdit tables.
Fixing REL gene coord display.
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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''parE''  
''parE''  
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3021, b3030, JW2998, nfxD''<ref name='LIB:Riley_2006'/>
''ECK3021, b3030, JW2998, nfxD''<ref name='LIB:Riley_2006'/>
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{|  id="F46a9ebeb927d0"  class=" tableEdit Gene_location_table"   
{|  id="F46a9ebeb927d0"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 3107676..3109568<br />{{GBrowseFigureByCoord|3107676|3109568|REL606|NC_012967}}
NC_012967: 3109568..3107676<br />{{GBrowseFigureByCoord|3107676|3109568|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|3107676|3109568|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3107676|3109568|GBrowse (REL606)}}
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{|  id="C46a9ebec4fe18"  class=" tableEdit Gene_sequence_features_table"   
{|  id="C46a9ebec4fe18"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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{| {{Prettytable}}  id="G46a9ebec9748d"  class=" tableEdit Gene_allele_table"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments


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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
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!|Name!!URL!!Comments
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Revision as of 20:40, 21 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

parE

Mnemonic
Synonyms

ECK3021, b3030, JW2998, nfxD[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

68.36 minutes 

MG1655: 3173418..3171526
gbrowse_img.php?coord=3171526..3173418&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3109568..3107676
gbrowse_img.php?coord=3107676..3109568&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3174052..3172160
gbrowse_img.php?coord=3172160..3174052&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3271163..3269271
gbrowse_img.php?coord=3269271..3271163&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
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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

JW2998

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCACGCAAACTTATAACGCTGA

Primer 2:CCAACCTCAATCTCCGCCATGTC

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[3]

est. P1 cotransduction: 46% [4]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[3]

est. P1 cotransduction: 80% [4]

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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:EG10687

EchoBASE (EcoliWiki Page)

EchoBASE:EB0681

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3030

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3776

EcoGene (EcoliWiki Page)

EcoGene:EG10687

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PARE

CGSC (EcoliWiki Page)

CGSC:33451

ASAP (EcoliWikiPage)

ASAP:ABE-0009950


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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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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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