yncK 2:Gene: Difference between revisions

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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''yncK_2''  
''yncK_2''  
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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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''yncK, ECK1425, b4530, JW5227, b4531, JW5961, b4578, JW5227+JW5961, yncK_1''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
''yncK, ECK1425, b4530, JW5227, b4531, JW5961, b4578, JW5227+JW5961, yncK_1''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><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|1501167|1501334|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10557 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10557 EcoCyc Sequence Dump]  
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W3110
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MG1655
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10557 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10557 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1500386|1502673|GBrowse(MG1655)}}
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*[http://biocyc.org/ECOLI/sequence?object=G0-10557 EcoCyc Sequence Dump]  
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W3110
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W3110: 1505363..1505076<br />{{GBrowseFigureByCoord|1504076|1506363|ecoli_W3110|W3110}}  
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MG1655
MG1655
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10557 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10557 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1500167|1502673|GBrowse(MG1655)}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1500167..1502673 GBrowse(MG1655)]
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1501167|1501673|FASTA Dump}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1501167..1501673&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G0-10557 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10557 EcoCyc Sequence Dump]  
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W3110
W3110
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W3110: 1505363..1504857<br />{{GBrowseFigureByCoord|1503857|1506363|ecoli_W3110|W3110}}  
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{{GBrowseLink|ecoli_W3110|AC_000091|1503857|1506363|GBrowse(W3110)}}
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1504857..1505363&plugin_action=Go FASTA Dump]
 
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|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
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[[cgscmutation:105790|CGSC:105790]]
[[cgscmutation:105790|CGSC:105790]]
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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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[[trg:Gene|trg-2::Tn10]]
[[trg:Gene|trg-2::Tn10]]
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est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 78% <ref name='LIB:Nichols_linked_Tn'/>  
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[[yddE:Gene|zdd-235::Tn10]]
[[yddE:Gene|zdd-235::Tn10]]
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CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<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:zdc-235::Tn10


Synonyms:zdc-235::Tn10
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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=0285052&formSubmitReturn=1 ASAP:ABE-0285052]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0285052&formSubmitReturn=1 ASAP:ABE-0285052]
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==References==
==References==
{{BacktoTop}}
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<references/>
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__NOTOC__
__NOTOC__

Revision as of 18:34, 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

yncK_2

Mnemonic
Synonyms

yncK, ECK1425, b4530, JW5227, b4531, JW5961, b4578, JW5227+JW5961, yncK_1[1][2][3]

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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

32.36 minutes 

MG1655: 1501334..1501167
gbrowse_img.php?coord=1500167..1502334&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1505024..1504857
gbrowse_img.php?coord=1503857..1506024&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

MG1655

32.36 minutes 

MG1655: 1501673..1501386
gbrowse_img.php?coord=1500386..1502673&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1505363..1505076
gbrowse_img.php?coord=1504076..1506363&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

MG1655

 

MG1655: 1501673..1501167
gbrowse_img.php?coord=1500167..1502673&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1505363..1504857
gbrowse_img.php?coord=1503857..1506363&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

ΔyncK721::kan

PMID:16738554[4]

CGSC:105790


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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[5]

Status:

Primer 1:

Primer 2:

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[6]

est. P1 cotransduction: 78% [7]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[6]

est. P1 cotransduction: 25% [7]nnSynonyms:zdc-235::Tn10

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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:G0-10557

EcoGene (EcoliWiki Page)

EcoGene:EG14359

ASAP (EcoliWikiPage)

ASAP:ABE-0285051

ASAP (EcoliWikiPage)

ASAP:ABE-0285052


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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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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
  5. ↑ 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  7. ↑ 7.0 7.1 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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