tfaS:Gene: Difference between revisions

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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''tfaS''  
''tfaS''  
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK2347, b2353, JW5383, yfdJ''<ref name='LIB:Riley_2006'/>
''ECK2347, b2353, JW5383, yfdJ''<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|2468825|2469127|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|2468825|2469127|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7222 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7222 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2476249|2476551|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2476249|2476551|FASTA Dump}}  
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!Feature type!!Location!!Description
!|Feature type!!Location!!Description
 
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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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&Delta;tfaS (Keio:JW5383)
&Delta;tfaS (Keio:JW5383)
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|[[PMID:16738554]]<ref name=PMID:16738554/>
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[[PMID:16738554]]<ref name=PMID:16738554/>
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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JW5383
JW5383
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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:CCtTCCTCCGGCAGTTCAGGCCA  
Primer 2:CCtTCCTCCGGCAGTTCAGGCCA  
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[[yfbO:Gene|zfb-223::Tn10]]
[[yfbO:Gene|zfb-223::Tn10]]
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CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zej-223::Tn10  
Synonyms:zej-223::Tn10  
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zfd-1::Tn10
zfd-1::Tn10
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CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 43% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 43% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfb-1::Tn10


Synonyms:zfb-1::Tn10
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7222 EcoCyc:G7222]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7222 EcoCyc:G7222]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3886 EchoBASE:EB3886]
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3886 EchoBASE:EB3886]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2353 EcoliGenExpDB:b2353]
[http://chase.ou.edu/macro/searchlink.php?bnum=b2353 EcoliGenExpDB:b2353]
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|-
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
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[http://ecogene.org/geneinfo.php?eg_id=EG14134 EcoGene:EG14134]
[http://ecogene.org/geneinfo.php?eg_id=EG14134 EcoGene:EG14134]
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|-
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
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[http://BioCyc.org/ECOO157/new-image?object=Z2983 ECOO157CYC:Z2983]
[http://BioCyc.org/ECOO157/new-image?object=Z2983 ECOO157CYC:Z2983]
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Revision as of 18:27, 29 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

tfaS

Mnemonic
Synonyms

ECK2347, b2353, JW5383, yfdJ[1]

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

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

53.21 minutes 

MG1655: 2468825..2469127
gbrowse_img.php?coord=2467825..2470127&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2476249..2476551
gbrowse_img.php?coord=2475249..2477551&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

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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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

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

ΔtfaS (Keio:JW5383)

deletion

deletion

PMID:16738554[2]

Shigen


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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

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

JW5383

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCCGTCCCGCGACTATCGCCCC

Primer 2:CCtTCCTCCGGCAGTTCAGGCCA

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[4]

est. P1 cotransduction: % [5]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[4]

est. P1 cotransduction: 43% [5]
Synonyms:zfb-1::Tn10

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See Help:Gene_resources for help entering information into the Genetic Resources table.

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:G7222

EchoBASE (EcoliWiki Page)

EchoBASE:EB3886

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2353

EcoGene (EcoliWiki Page)

EcoGene:EG14134

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z2983


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Notes

Links

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Name URL Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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