secF:Gene: Difference between revisions

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!{{table_heading_style}} |Standard name
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''secF''  
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!{{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |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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MG1655
MG1655
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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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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|428729|429700|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|428729|429700|FASTA Dump}}  
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JW0399
JW0399
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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|[[PMID:16769691]]<ref name=PMID:16769691/>
[[PMID:16769691]]<ref name=PMID:16769691/>


Status:Clone OK
Status:Clone OK
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Primer 2:CCCGGCAGAATTGACGGCTGATC  
Primer 2:CCCGGCAGAATTGACGGCTGATC  
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[[yaiU:Gene|zai-3053::Tn10]]
[[yaiU:Gene|zai-3053::Tn10]]
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CAG18091 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39364 CGSC7336]<ref name='LIB:cgsc'/>
CAG18091 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39364 CGSC7336]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zaj-3053::Tn10 nnnCAG18091 also carries proC9999 (CGSC).  
 
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Synonyms:zaj-3053::Tn10  
 
 
CAG18091 also carries proC9999 (CGSC).  
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[[tsx:Gene|tsx-247::Tn10]]
[[tsx:Gene|tsx-247::Tn10]]
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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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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001419&formSubmitReturn=1 ASAP:ABE-0001419]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001419&formSubmitReturn=1 ASAP:ABE-0001419]
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==References==
==References==
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<references/>
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__NOTOC__
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Revision as of 18:35, 21 January 2009

{{#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=427729..430700&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 428729..429700
gbrowse_img.php?coord=427729..430700&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

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]nnSynonyms: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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Name URL Comments
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References

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  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).


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