ryeB: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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''ryeB''  
''ryeB''  
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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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''ECK1839, b4433, JWR0238, tpke79, tkpe79''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK1839, b4433, JWR0238, tpke79, tkpe79''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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===Notes===
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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|1921188|1921308|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|1921188|1921308|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-8883 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-8883 EcoCyc Sequence Dump]  
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W3110
W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1924878|1924998|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1924878|1924998|FASTA Dump}}  
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===Notes===
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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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:
Status:
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Primer 2:  
Primer 2:  
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[[yeaI:Gene|zea-225::Tn10]]
[[yeaI:Gene|zea-225::Tn10]]
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CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
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est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zdj-225::Tn10  
 
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[[eda:Gene|eda-51::Tn10]]
[[eda:Gene|eda-51::Tn10]]
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est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>  
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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=G0-8883 EcoCyc:G0-8883]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-8883 EcoCyc:G0-8883]
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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=EB4515 EchoBASE:EB4515]
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4515 EchoBASE:EB4515]
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<noinclude><protect>
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==References==
==References==
{{BacktoTop}}
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<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:15, 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

ryeB

Mnemonic
Synonyms

ECK1839, b4433, JWR0238, tpke79, tkpe79[1][2]

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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

41.41 minutes, 41.41 minutes 

MG1655: 1921308..1921188
gbrowse_img.php?coord=1920188..1922308&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1924998..1924878
gbrowse_img.php?coord=1923878..1925998&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
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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

Plasmid clone

Shigen

PMID:16769691[3]

Status:

Primer 1:

Primer 2:

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[4]

est. P1 cotransduction: 9% [5]nnSynonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[4]

est. P1 cotransduction: 74% [5]

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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:G0-8883

EchoBASE (EcoliWiki Page)

EchoBASE:EB4515


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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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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