secF:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''secF''  
''secF''  
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!align=left {{table_heading_style}} |Mnemonic
!align=left |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
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''ECK0403, b0409, JW0399''<ref name='LIB:Riley_2006'/>
''ECK0403, b0409, JW0399''<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|428729|429700|FASTA Dump}}
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*[http://biocyc.org/ECOLI/sequence?object=EG10940 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10940 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 397928..398899<br />{{GBrowseFigureByCoord|397928|398899|REL606|NC_012967}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|366118|370973|FASTA Dump}}  
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[[REL606]]
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NC_012967: 397928..398899<br />{{GBrowseFigureByCoord|397928|398899|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|397928|398899|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|397928|398899|FASTA Dump}}


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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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est. P1 cotransduction: 91% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 91% <ref name='LIB:Nichols_linked_Tn'/>  


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Revision as of 00:38, 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

secF

Mnemonic
Synonyms

ECK0403, b0409, JW0399[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

9.24 minutes 

MG1655: 428729..429700
gbrowse_img.php?coord=428729..429700&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 397928..398899
gbrowse_img.php?coord=397928..398899&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 428729..429700
gbrowse_img.php?coord=428729..429700&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 368060..369031
gbrowse_img.php?coord=368060..369031&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

secF62(Cs)

cold sensitive

CGSC:38552


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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

JW0399

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCGCACAGGAATATACTGTTGA

Primer 2:CCCGGCAGAATTGACGGCTGATC

zai-3053::Tn10

Linked marker

CAG18091 = CGSC7336[3]

est. P1 cotransduction: 25% [4]
Synonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).

tsx-247::Tn10

Linked marker

CAG12148 = CGSC7337[3]

est. P1 cotransduction: 91% [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:EG10940

EchoBASE (EcoliWiki Page)

EchoBASE:EB0933

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0409

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0519

EcoGene (EcoliWiki Page)

EcoGene:EG10940

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:SECF

CGSC (EcoliWiki Page)

CGSC:29893

ASAP (EcoliWikiPage)

ASAP:ABE-0001419


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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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