allR:Gene: Difference between revisions

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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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Revision as of 22:16, 10 May 2010

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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

allR

Mnemonic

Allantoin

Synonyms

ECK0499, b0506, JW0494, gclR, glxA3, ybbU[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

11.47 minutes 

MG1655: 532235..533050
gbrowse_img.php?coord=532235..533050&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 505177..505992
gbrowse_img.php?coord=505177..505992&genome=REL606&name=NC_012967&trackset=0&width=300&.png

BW2952

NC_012759: 434994..435809
gbrowse_img.php?coord=434994..435809&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 532235..533050
gbrowse_img.php?coord=532235..533050&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 471566..472381
gbrowse_img.php?coord=471566..472381&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 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

allRM141A

M141A

No effect on repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRC142W

C142W

Strongly reduced repressor activity. Reduces DNA binding. Prevents assembly into functionally active tetramers

seeded from UniProt:P0ACN4

allRCKSMVRMC135APA

CKSMVRMC135APA

Loss of repressor activity. Loss of DNA binding. Reduces assembly into functionally active tetramers

seeded from UniProt:P0ACN4

allRS236A,M

S236A,M

Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRC217A,S

C217A,S

Slightly reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRL215A

L215A

Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

allRS234A,N

S234A,N

Reduced repressor activity. Loss of glyoxylate-triggered dissociation from DNA

seeded from UniProt:P0ACN4

ΔallR (Keio:JW0494)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8639[3]

ΔallR789::kan

PMID:16738554[2]

CGSC:99978


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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

JW0494

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCACGGAAGTTAGACGGCGCGG

Primer 2:CCTGGATGTGCTTTCAGTCCCAA

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 29% [5]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

purK79::Tn10

Linked marker

CAG12171 = CGSC7342[3]

est. P1 cotransduction: 49% [5]
Synonyms:purE79::Tn10

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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:G6276

EchoBASE (EcoliWiki Page)

EchoBASE:EB3382

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0506

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0621

EcoGene (EcoliWiki Page)

EcoGene:EG13616

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBBU

ASAP (EcoliWikiPage)

ASAP:ABE-0001750


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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 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. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 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
  5. ↑ 5.0 5.1 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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