elfD:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46a9bc1be6994"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6481 ECOCYC:G6481]
EcoCyc:G6481
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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]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13710 EcoGene:EG13710]
EcoGene:EG13710
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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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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120003081
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3474
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0003187
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:15, 27 May 2013

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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

elfD

Mnemonic

Systematic nomenclature

Synonyms

ycbR, ECK0930, b0939, JW0922[1], JW0922

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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

21.5 minutes 

MG1655: 997713..998414
<gbrowseImage> name=NC_000913:997713..998414 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1015581..1016282
<gbrowseImage> name=NC_012967:1015581..1016282 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 900681..901382
<gbrowseImage> name=NC_012759:900681..901382 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 998912..999613
<gbrowseImage> name=AC_000091:998912..999613 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1051641..1052342
<gbrowseImage> name=NC_010473:1051641..1052342 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

ΔycbR (Keio:JW0922)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8931[3]

ΔycbR755::kan

PMID:16738554[2]

CGSC:103930


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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

JW0922

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAACTTGCATAACAAAGGG

Primer 2:CCCGATTTACAGTTGAGTTGCGG

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[3]

est. P1 cotransduction: 9% [5]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[3]

est. P1 cotransduction: 86% [5]

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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:G6481

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13710

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946773

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003081

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3474

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003187

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. ↑ 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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