yebV: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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W3110: 1923494..1923730<br /><gbrowseImage>
W3110: 1923494..1923730<br /><gbrowseImage>
name=AC_000091:1923494..1923730
name=NC_007779:1923494..1923730
source=W3110
source=W3110
preset=GeneLocation
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{{GBrowseLink|W3110|AC_000091|1922494|1924730|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1922494|1924730|GBrowse(W3110)}}  
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{{GBrowseFastaLink|W3110|AC_000091|1923494|1923730|FASTA Dump}}  
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9d00ee7a63"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="X46a9d00f37649"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="X46a9d00f37649"  class=" tableEdit Gene_allele_table dataTable"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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yebV
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deletion
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Sensitivity to
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increases sensitivity to bicyclomycin
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PMID:21357484
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fig 2


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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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EcoCyc:G7009
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[[EcoGene]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7009 ECOCYC:G7009]
EcoGene:EG14024
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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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG14024 EcoGene:EG14024]
RegulonDB:ECK120003596
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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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[[EchoBASE]]
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EchoBASE:EB3778
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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-0006110
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:39, 19 September 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

yebV

Mnemonic

Systematic nomenclature

Synonyms

ECK1835, b1836, JW5302[1], JW5302

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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

41.38 minutes, 41.38 minutes 

MG1655: 1919804..1920040
<gbrowseImage> name=NC_000913:1919804..1920040 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1900357..1900593
<gbrowseImage> name=NC_012967:1900357..1900593 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1811863..1812099
<gbrowseImage> name=NC_012759:1811863..1812099 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1923494..1923730
<gbrowseImage> name=NC_007779:1923494..1923730 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2010375..2010611
<gbrowseImage> name=NC_010473:2010375..2010611 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

ΔyebV (Keio:JW5302)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11308[3]

ΔyebV761::kan

PMID:16738554[2]

CGSC:104430

yebV

deletion

Sensitivity to

increases sensitivity to bicyclomycin

PMID:21357484[4]

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

JW5302

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAAACCAGTGTGCGCATAGG

Primer 2:CCGGCAAGACGCATAATCCAGGC

19H3

Kohara Phage

Genobase

PMID:3038334[6]

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[3]

est. P1 cotransduction: 10% [7]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[3]

est. P1 cotransduction: 70% [7]

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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:G7009

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14024

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003596

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946347

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3778

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0006110

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. ↑ 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. ↑ 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 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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