secF:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 17:04, 24 June 2011

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions 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

Secretory

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
<gbrowseImage> name=NC_000913:428729..429700 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 397928..398899
<gbrowseImage> name=NC_012967:397928..398899 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 331488..332459
<gbrowseImage> name=NC_012759:331488..332459 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 428729..429700
<gbrowseImage> name=AC_000091:428729..429700 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 368060..369031
<gbrowseImage> name=NC_010473:368060..369031 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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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 Strain Genomic Location Evidence Reference Notes
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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 Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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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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