gapC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
!align=left |Standard name
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''gapC''  
''gapC''  
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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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Note that this is a pseudogene in K12 strains.
Note that this is a pseudogene in K12 strains.
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''gapC, ECK1409, b1416, JW1413, b1417, JW5906, b4493, JW5906+JW1413, gapC_2'', gapC_1<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'', gapC_1<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>


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*{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491427|1492427|FASTA Dump}}<br \>  
*{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491427|1492427|FASTA Dump}}<br \>  


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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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Revision as of 01:17, 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

gapC

Mnemonic
Synonyms

Note that this is a pseudogene in K12 strains.

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

32.07 minutes 

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

W3110

 

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

MG1655

32.07 minutes 

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

W3110

 

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

MG1655

 

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

W3110

 

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

gapC_2

PMID:12519969[4]

ASAP

At position 128 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20314

gapC_2

PMID:12519969[4]

ASAP

At position 128 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20315

ΔgapC777::kan

PMID:16738554[5]

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[6]

Status:

Primer 1:

Primer 2:

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[7]

est. P1 cotransduction: 7% [8]

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[7]

est. P1 cotransduction: 82% [8]

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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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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. ↑ 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. ↑ 4.0 4.1 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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).

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