lexA:Gene: Difference between revisions

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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=635 Genobase]
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=635 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:1E4|1E4]]
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Kohara Phage
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=636 Genobase]
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PMID:3038334


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!|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=EG10533 EcoCyc:EG10533]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0528 EchoBASE:EB0528]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b4043 EcoliGenExpDB:b4043]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C5014 ECOL199310CYC:C5014]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG10533 EcoGene:EG10533]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=LEXA ECOO157CYC:LEXA]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/558 CGSC:558]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013241&formSubmitReturn=1 ASAP:ABE-0013241]
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Revision as of 20:35, 21 September 2011

{{#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 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

lexA

Mnemonic

Lambda excision

Synonyms

ECK4035, b4043, JW4003, exrA, tsl, umuA[1]

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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

91.71 minutes 

MG1655: 4255138..4255746
<gbrowseImage> name=NC_000913:4255138..4255746 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4236047..4236655
<gbrowseImage> name=NC_012967:4236047..4236655 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4193983..4194591
<gbrowseImage> name=NC_012759:4193983..4194591 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4260705..4261313
<gbrowseImage> name=AC_000091:4260705..4261313 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4354834..4355442
<gbrowseImage> name=NC_010473:4354834..4355442 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

A description of the lexA gene may be found in Markham et al. (1981)[2].

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

lexAG85D

G85D

(in lexA3, resistant to cleavage)

Strain variation; seeded from UniProt:P0A7C2

lexA107

CGSC:6267

lexA1(Ind-)

non-inducible SOS response

CGSC:9237

lexA41(ts)

temperature sensitive

CGSC:9601

lexA3(Ind-)

non-inducible SOS response

CGSC:9602

lexA51

CGSC:10280

lexA101

CGSC:11964

lexA102

CGSC:11979

lexA109

CGSC:11985

lexA103

CGSC:14425

lexA104

CGSC:14427

lexA105

CGSC:14429

lexA106

CGSC:14431

lexA108

CGSC:14439

lexA71::Tn5

CGSC:30813

lexA2

C461T

T154I

Sensitivity to

hypocleavable repressor leads to a sensitivity to DNA damage

PMID:3127383[3]

spr

PMID:2834329[4] PMID:7038393[5]

uninducible, not cleaved during SOS response

lexA264 (Silent SalI site )

GGT->GTT

G80V

Ind- phenotype

PMID:2834329[4]

Formic acid was used as the mutagen

lexA261 (Silent SalI site )

GGT->GAT

G80D

Ind- phenotype

PMID:2834329[4]

Hydroxylamine was used as the mutagen

lexA266 (Silent SalI site )

GTG->GAG

V82E

Ind- phenotype

PMID:2834329[4]

Formic acid was used as the mutagen

lexA265 (Silent SalI site )

GTG->ATG

V82M

Ind- phenotype

PMID:2834329[4]

Both formic acid and hydroxylamine were used as to mutagenize the strain.

lexA262 (Silent SalI site )

GCT->GTT

A83V

Ind- phenotype

PMID:2834329[4]

Hydroxylamine were used as to mutagenize the strain.

lexA267 (Silent SalI site )

GCT->ACT

A83T

Ind- phenotype

PMID:2834329[4]

Both hydroxylamine and hydrazine were used as to mutagenize the strain.

lexA252 (Silent SalI site )

GCT->--

A83Δ

Ind- phenotype

PMID:2834329[4]

Spontaneous mutation

lexA260 (Silent SalI site )

GCC->ACC

A84T

Ind- phenotype

PMID:2834329[4]

Hydroxylamine was used as to mutagenize the strain.

lexA268 (Silent SalI site )

GCC->GAC

A84D

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA3 (Silent SalI site )

GGT->GAT

G85D

Ind- phenotype

PMID:2834329[4]

Hydrazine was used as to mutagenize the strain.

lexA252 (Silent SalI site )

GAA->AAA

A95K

Ind- phenotype

PMID:2834329[4]

Spontaneous mutation

lexA274 (Silent SalI site )

GGC->CCC

R114P

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA251 (Silent SalI site )

TCG->TTG

S119L

Ind- phenotype

PMID:2834329[4]

This allele was produced spontaneously and using hydroxylamine.

lexA269 (Silent SalI site )

GTC->TTC

V115F

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA280 (Silent SalI site )

ATG->TTG

M120L

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA263 (Silent SalI site )

GGG->GAG

G117E

Ind- phenotype

PMID:2834329[4]

Both formic acid and hydroxylamine were used as to mutagenize the strain.

lexA259 (Silent SalI site )

ACC->ATC

T154I

Ind- phenotype

PMID:2834329[4]

Both hydrazine and hydroxylamine were used as to mutagenize the strain.

lexA270 (Silent SalI site )

AAG->AGG

K156R

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA272 (Silent SalI site )

AAG->ATG

K156M

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA271-281

K156N/Q184H

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA271 (Silent SalI and BglI site)

AAG->AAT

K156N

Ind- phenotype

PMID:2834329[4]

lexA281 (Silent SalI and BstI site)

CAG->CAT

Q184H

Ind- phenotype

PMID:2834329[4]

lexA273-282

K156T/E184V

Ind- phenotype

PMID:2834329[4]

Formic acid was used as to mutagenize the strain.

lexA273 (Silent SalI and BglI sites)

AAG->ACG

K156T

Ind- phenotype

PMID:2834329[4]

lexA282 (Silent SalI and BglI sites)

GAA->GTA

E170V

Ind- phenotype

PMID:2834329[4]

lexA3 (del) in MDS 42

Sensitivity to

increases senstitivity to bicyclomycin

PMID:21183718[6]

fig. 2


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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

JW4003

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAAAGCGTTAACGGCCAGGCA

Primer 2:CCaAGCCAGTCGCCGTTGCGAAT

1F8

Kohara Phage

Genobase

PMID:3038334[8]

12B4

Kohara Phage

Genobase

PMID:3038334[8]

1E4

Kohara Phage

Genobase

PMID:3038334[8]

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[9]

est. P1 cotransduction: 60% [10]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[9]

est. P1 cotransduction: 9% [10]

DM Strain List

Strain

There are several strains with single lexA mutations listed in Table 1.

PMID:4343824[11]

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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
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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. ↑ Markham, BE et al. (1981) Nucleotide sequence of the lexA gene of Escherichia coli K-12. Nucleic Acids Res. 9 4149-61 PubMed
  3. ↑ Peterson, KR et al. (1988) The Escherichia coli K-12 lexA2 gene encodes a hypocleavable repressor. J. Bacteriol. 170 1975-7 PubMed
  4. ↑ 4.00 4.01 4.02 4.03 4.04 4.05 4.06 4.07 4.08 4.09 4.10 4.11 4.12 4.13 4.14 4.15 4.16 4.17 4.18 4.19 4.20 4.21 4.22 4.23 4.24 4.25 Lin, LL & Little, JW (1988) Isolation and characterization of noncleavable (Ind-) mutants of the LexA repressor of Escherichia coli K-12. J. Bacteriol. 170 2163-73 PubMed
  5. ↑ Froehlich, B (1981) Weigle reactivation of the single-stranded DNA phage f1. Mol. Gen. Genet. 184 416-20 PubMed
  6. ↑ Washburn, RS & Gottesman, ME (2011) Transcription termination maintains chromosome integrity. Proc. Natl. Acad. Sci. U.S.A. 108 792-7 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 8.2 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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).
  11. ↑ Mount, DW et al. (1972) Dominant mutations (lex) in Escherichia coli K-12 which affect radiation sensitivity and frequency of ultraviolet lght-induced mutations. J. Bacteriol. 112 886-93 PubMed

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