rhaT:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''rhaT''  
''rhaT''  
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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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''ECK3900, b3907, JW3878''<ref name='LIB:Riley_2006'/>
''ECK3900, b3907, JW3878''<ref name='LIB:Riley_2006'/>


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{{GBrowseFastaLink|ecoli|NC_000913|4097514|4098548|FASTA Dump}}
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*[http://biocyc.org/ECOLI/sequence?object=EG11313 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11313 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 4078973..4080007<br />{{GBrowseFigureByCoord|4078973|4080007|REL606|NC_012967}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4195143|4200313|FASTA Dump}}  
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NC_012967: 4078973..4080007<br />{{GBrowseFigureByCoord|4078973|4080007|REL606|NC_012967}}
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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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Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).  
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).  


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Revision as of 05:36, 9 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

rhaT

Mnemonic
Synonyms

ECK3900, b3907, JW3878[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

88.31 minutes 

MG1655: 4098548..4097514
gbrowse_img.php?coord=4097514..4098548&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4078973..4080007
gbrowse_img.php?coord=4078973..4080007&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3536156..3537190
gbrowse_img.php?coord=3536156..3537190&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4198245..4197211
gbrowse_img.php?coord=4197211..4198245&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

ΔrhaT (Keio:JW3878)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10797[3]

ΔrhaT767::kan

PMID:16738554[2]

CGSC:102688


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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

JW3878

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGTAACGCGATTACGATGGG

Primer 2:CCATTCGCCATGCCGATGCCGAC

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[3]

est. P1 cotransduction: 27% [5]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[3]

est. P1 cotransduction: 13% [5]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG11313

EchoBASE (EcoliWiki Page)

EchoBASE:EB1289

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3907

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4857

EcoGene (EcoliWiki Page)

EcoGene:EG11313

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RHAT

CGSC (EcoliWiki Page)

CGSC:34185

ASAP (EcoliWikiPage)

ASAP:ABE-0012749


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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. ↑ 2.0 2.1 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. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 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
  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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