nfi:Gene

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Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

nfi

Mnemonic

Endonuclease V

Synonyms

ECK3990, b3998, JW5547, yjaF, yfaF[1][2]

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Notes

Location(s) and DNA Sequence

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<protect> 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

90.45 minutes, 90.45 minutes 

MG1655: 4196813..4197484
<gbrowseImage> name=NC_000913:4196813..4197484 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4178402..4179073
<gbrowseImage> name=NC_012967:4178402..4179073 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4086493..4087164
<gbrowseImage> name=NC_012759:4086493..4087164 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3437891..3437220
<gbrowseImage> name=NC_007779:3437220..3437891 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4296509..4297180
<gbrowseImage> name=NC_010473:4296509..4297180 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

Coding Start (SO:0000323)

MG1655

4196813

Edman degradation

PMID:8990280[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

Δnfi (Keio:JW5547)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC11458[5]

Δnfi-769::kan

PMID:16738554[4]

CGSC:102048


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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

JW5547

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGATCTCGCGTCATTACGCGC

Primer 2:CCGGGCTGATTTGCTGTATAGCG

7B7

Kohara Phage

Genobase

PMID:3038334[7]

thiC39::Tn10

Linked marker

CAG18500 = CGSC7472[5]

est. P1 cotransduction: 92% [8]
Synonyms:thi-39::Tn10

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[5]

est. P1 cotransduction: 15% [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

EcoCyc:EG11915

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11915

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001843

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948502

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1859

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013068

Escherichia coli str. K-12 substr. MG1655

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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. Guo, G et al. (1997) nfi, the gene for endonuclease V in Escherichia coli K-12. J. Bacteriol. 179 310-6 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. 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  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. 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
  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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