parC:Gene: Difference between revisions

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Fixing REL gene coord display.
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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''parC''  
''parC''  
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!align=left |Mnemonic
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partitioning of the nucleoid
partitioning of the nucleoid
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3010, b3019, JW2987''<ref name='LIB:Riley_2006'/>
''ECK3010, b3019, JW2987''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 3097887..3100145<br />{{GBrowseFigureByCoord|3097887|3100145|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|3097887|3100145|GBrowse (REL606)}}
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Revision as of 20:40, 21 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

parC

Mnemonic

partitioning of the nucleoid

Synonyms

ECK3010, b3019, JW2987[1]

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Notes

The partitioning defect comes from the inability of these cells to partition the nucleoids into daughter cells. This results in filamentous cells with a cluster of nucleoid at the center and subsequent DNA-free cells.

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

68.15 minutes 

MG1655: 3163995..3161737
gbrowse_img.php?coord=3161737..3163995&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3100145..3097887
gbrowse_img.php?coord=3097887..3100145&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3164629..3162371
gbrowse_img.php?coord=3162371..3164629&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3261740..3259482
gbrowse_img.php?coord=3259482..3261740&genome=ecoli_DH10B&name=DH10B&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

parC1215

G2199A

G703D

Growth Phenotype

ts @ 42

PMID:2170028[2], PMID:2842295[3]

actual nucleotide mapping was referenced in [2]

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Notes

The Keio collection[4] lists a deletion of parC, which is an essential gene. The insertion in this strain probably traps a duplication of the parC region.

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

JW2987

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAGCGATATGGCAGAGCGCCT

Primer 2:CCtTCTTCGCTATCACCGCTGCT

metC162::Tn10

Linked marker

CAG18475 = CGSC7435[6]

est. P1 cotransduction: 67% [7]

tolC210::Tn10

Linked marker

CAG12184 = CGSC7437[6]

est. P1 cotransduction: 56% [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:EG10686

EchoBASE (EcoliWiki Page)

EchoBASE:EB0680

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3019

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3760

EcoGene (EcoliWiki Page)

EcoGene:EG10686

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:PARC

CGSC (EcoliWiki Page)

CGSC:33440

ASAP (EcoliWikiPage)

ASAP:ABE-0009916


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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. ↑ 2.0 2.1 Kato, J et al. (1990) New topoisomerase essential for chromosome segregation in E. coli. Cell 63 393-404 PubMed
  3. ↑ Kato, J et al. (1988) Gene organization in the region containing a new gene involved in chromosome partition in Escherichia coli. J. Bacteriol. 170 3967-77 PubMed
  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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