gapC:Gene: Difference between revisions

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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
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''gapC_1''  
''gapC_1''  
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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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''gapC, ECK1409, b1416, JW1413, b1417, JW5906, b4493, JW5906+JW1413, gapC_2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
''gapC, ECK1409, b1416, JW1413, b1417, JW5906, b4493, JW5906+JW1413, gapC_2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
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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|1487737|1487988|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|1487737|1487988|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
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W3110
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491427|1491678|FASTA Dump}}  
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MG1655
MG1655
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1486985|1489737|GBrowse(MG1655)}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1486985..1489737 GBrowse(MG1655)]
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1487985|1488737|FASTA Dump}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1487985..1488737&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
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W3110
W3110
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W3110: 1492427..1491675<br />{{GBrowseFigureByCoord|1490675|1493427|ecoli_W3110|W3110}}  
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{{GBrowseLink|ecoli_W3110|AC_000091|1490675|1493427|GBrowse(W3110)}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1490675..1493427 GBrowse(W3110)]
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491675|1492427|FASTA Dump}}
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MG1655
MG1655
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1486737|1489737|GBrowse(MG1655)}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1486737..1489737 GBrowse(MG1655)]
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1487737|1488737|FASTA Dump}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1487737..1488737&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]  
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W3110
W3110
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W3110: 1492427..1491427<br />{{GBrowseFigureByCoord|1490427|1493427|ecoli_W3110|W3110}}  
W3110: 1492427..1491427<br />{{GBrowseFigureByCoord|1490427|1493427|ecoli_W3110|W3110}}  
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{{GBrowseLink|ecoli_W3110|AC_000091|1490427|1493427|GBrowse(W3110)}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1490427..1493427 GBrowse(W3110)]
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491427|1492427|FASTA Dump}}
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1491427..1492427&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:101092|CGSC:101092]]
[[cgscmutation:101092|CGSC:101092]]
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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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[[ompN:Gene|zhj-3076::Tn10]]
[[ompN:Gene|zhj-3076::Tn10]]
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est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>  
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[[trg:Gene|trg-2::Tn10]]
[[trg:Gene|trg-2::Tn10]]
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est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/>  
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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=0004727&formSubmitReturn=1 ASAP:ABE-0004727]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004727&formSubmitReturn=1 ASAP:ABE-0004727]
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==References==
==References==
{{BacktoTop}}
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__NOTOC__
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Revision as of 18:35, 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

gapC_1

Mnemonic
Synonyms

gapC, ECK1409, b1416, JW1413, b1417, JW5906, b4493, JW5906+JW1413, gapC_2[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

32.07 minutes 

MG1655: 1487988..1487737
gbrowse_img.php?coord=1486737..1488988&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1491678..1491427
gbrowse_img.php?coord=1490427..1492678&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

MG1655

32.07 minutes 

MG1655: 1488737..1487985
gbrowse_img.php?coord=1486985..1489737&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1492427..1491675
gbrowse_img.php?coord=1490675..1493427&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

MG1655

 

MG1655: 1488737..1487737
gbrowse_img.php?coord=1486737..1489737&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1492427..1491427
gbrowse_img.php?coord=1490427..1493427&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

ΔgapC777::kan

PMID:16738554[4]

CGSC:101092


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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:

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[6]

est. P1 cotransduction: 7% [7]

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[6]

est. P1 cotransduction: 82% [7]

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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:G8205

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1417

EcoGene (EcoliWiki Page)

EcoGene:EG12103

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:GAPC

ASAP (EcoliWikiPage)

ASAP:ABE-0004727


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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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