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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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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=EG11122 ECOCYC:EG11122]
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11122 EcoGene:EG11122]
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Escherichia coli str. K-12 substr. MG1655  
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RegulonDB:ECK120001106
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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EchoBASE:EB1112
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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ASAP:ABE-0004200
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:13, 27 May 2013

{{#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

yciB

Mnemonic

Systematic nomenclature

Synonyms

ECK1248, b1254, JW1246, ispA(S.f.)[1][2], ispA

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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

28.24 minutes 

MG1655: 1310914..1310375
<gbrowseImage> name=NC_000913:1310375..1310914 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1309945..1310484
<gbrowseImage> name=NC_012967:1309945..1310484 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1201224..1201763
<gbrowseImage> name=NC_012759:1201224..1201763 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1314604..1314065
<gbrowseImage> name=AC_000091:1314065..1314604 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1400310..1399771
<gbrowseImage> name=NC_010473:1399771..1400310 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

ΔyciB (Keio:JW1246)

deletion

deletion

PMID:16738554[3]

Shigen

yciB

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[4]

mutation didn't affect sensitivity to any of 22 other antibiotics tested. 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

JW1246

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAGCAGTTTCTTGATTTTTT

Primer 2:CCGGATTTATCTTCCTGCGGCAT

14C4

Kohara Phage

Genobase

PMID:3038334[6]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[7]

est. P1 cotransduction: 80% [8]
Synonyms:zch-506::Tn10, zci-506::Tn10

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[7]

est. P1 cotransduction: 78% [8]
Synonyms:trpB83::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

EcoCyc:EG11122

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11122

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946228

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001106

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1112

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004200

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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
  4. ↑ Tran, L et al. (2011) Single-gene deletion mutants of Escherichia coli with altered sensitivity to bicyclomycin, an inhibitor of transcription termination factor Rho. J. Bacteriol. 193 2229-35 PubMed
  5. ↑ 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
  6. ↑ 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  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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