rep:Gene: Difference between revisions

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Revision as of 21:39, 26 July 2010

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features 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

rep

Mnemonic

Replicase

Synonyms

ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?[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

85.32 minutes 

MG1655: 3958700..3960721
<gbrowseImage> name=NC_000913:3958700..3960721 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3922479..3924500
<gbrowseImage> name=NC_012967:3922479..3924500 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3848369..3850390
<gbrowseImage> name=NC_012759:3848369..3850390 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3676004..3673983
<gbrowseImage> name=AC_000091:3673983..3676004 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4057620..4059641
<gbrowseImage> name=NC_010473:4057620..4059641 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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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 Strain Genomic Location Evidence Reference Notes

Coding Start (SO:0000323)

MG1655

3958700

Edman degradation

PMID:2999067[3]


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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

Δrep (Keio:JW5604)

deletion

deletion

PMID:16738554[4]

Shigen

rep::Tn5KAN

PMID:12519969[5]

ASAP

At position 508 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB21451

Δrep::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire L-Aspartate

PMID:16095938[6]

Δrep::kan

deletion

Biolog:respiration

unable to respire L-Serine

PMID:16095938[6]

rep-5

CGSC:7013

rep-3

PMID:383240[7]

CGSC:9794

rep-142(ts)

temperature sensitive

CGSC:90737

[rep-71]

PMID:6286604[8]

CGSC:90823

null allele

Δrep-729::kan

PMID:16738554[4]

CGSC:113537


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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

JW5604

Plasmid clone

Shigen

PMID:16769691[9]

Status:cloned as old JW

Primer 1:GCCCGTCTAAACCCCGGCCAACA

Primer 2:CCTTTCCCTCGTTTTGCCGCCAT

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[10]

est. P1 cotransduction: 83% [11]
Synonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[10]

est. P1 cotransduction: 10% [11]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

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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:EG10837

EchoBASE (EcoliWiki Page)

EchoBASE:EB0830

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3778

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4698

EcoGene (EcoliWiki Page)

EcoGene:EG10837

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:REP

CGSC (EcoliWiki Page)

CGSC:303

ASAP (EcoliWikiPage)

ASAP:ABE-0012344


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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 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Bialkowska-Hobrzanska, H et al. (1985) Escherichia coli rep gene: identification of the promoter and N terminus of the rep protein. J. Bacteriol. 164 1004-10 PubMed
  4. ↑ 4.0 4.1 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. ↑ Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  6. ↑ 6.00 6.01 6.02 6.03 6.04 6.05 6.06 6.07 6.08 6.09 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  7. ↑ Takahashi, S et al. (1979) The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can. J. Biochem. 57 855-66 PubMed
  8. ↑ Tessman, I et al. (1982) Relative map location of the rep and rho genes of Escherichia coli. J. Bacteriol. 151 1637-40 PubMed
  9. ↑ 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
  10. ↑ 10.0 10.1 CGSC: The Coli Genetics Stock Center
  11. ↑ 11.0 11.1 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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