nikR:Gene: Difference between revisions

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''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>
''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>, yhhG''


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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11519 ECOCYC:EG11519]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11519 EcoGene:EG11519]
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Escherichia coli str. K-12 substr. MG1655
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://www.ncbi.nlm.nih.gov/gene?term=947995 GeneID:947995]
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Escherichia coli str. K-12 substr. MG1655


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Revision as of 20:57, 24 September 2011

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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 Interactions 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

nikR

Mnemonic

Nickel

Synonyms

ECK3465, b3481, JW3446, yhhG[1], yhhG

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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

77.95 minutes 

MG1655: 3616611..3617012
<gbrowseImage> name=NC_000913:3616611..3617012 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3549276..3549677
<gbrowseImage> name=NC_012967:3549276..3549677 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3505105..3505506
<gbrowseImage> name=NC_012759:3505105..3505506 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4021827..4021426
<gbrowseImage> name=AC_000091:4021426..4021827 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3714356..3714757
<gbrowseImage> name=NC_010473:3714356..3714757 source=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
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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

ΔnikR (Keio:JW3446)

deletion

deletion

PMID:16738554[2]

Shigen

nikRR3A

R3A

Loss of DNA-binding

seeded from UniProt:P0A6Z6

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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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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

JW3446

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCCAACGAGTCACCATCACGCT

Primer 2:CCATCTTCCTTCGGCAAGCACTG

10D10

Kohara Phage

Genobase

PMID:3038334[4]

5F2

Kohara Phage

Genobase

PMID:3038334[4]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[5]

est. P1 cotransduction: 38% [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: % [6]

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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:EG11519

Escherichia coli str. K-12 substr. MG1655

EcoGene (EcoliWiki Page)

EcoGene:EG11519

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947995

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ 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
  3. ↑ 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
  4. ↑ 4.0 4.1 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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