yjcC:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK4053, b4061, JW4022''<ref name='LIB:Riley_2006'/>
''ECK4053, b4061, JW4022''<ref name='LIB:Riley_2006'/>, JW4022''


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{|   id="N46aa0603a9430"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N46aa0603a9430"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11938 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11938 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|4272494|4276080|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4272494|4276080|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|4273494|4275080|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|4273494|4275080|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11938 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11938 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|4212339|NC_4213925|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|4212339|4213925|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|4212339|NC_4213925|FASTA Dump}}  
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W3110: 4279061..4280647<br /><gbrowseImage>
W3110: 4279061..4280647<br /><gbrowseImage>
name=AC_000091:4279061..4280647
name=NC_007779:4279061..4280647
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|4278061|4281647|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4278061|4281647|GBrowse(W3110)}}  
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{|   id="X46aa060470b3d"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46aa060470b3d"  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="G46aa0604bbeb7"  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="G46aa0604bbeb7"  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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''yjcC755(del)''::FRTKanFRT
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR12056
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Mutation was comparatively weak with decrease only happening to 33-67% of population.
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''yicC750''::FRTKanFRT
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR11978
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Mutation was comparatively weak with decrease only happening to 33-67% of population.
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''yjcC755(del)''::FRTKanFRT
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Sensitivity to
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An increase in UV Sensitivity
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR12056
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supplemental Table S7 & S1


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{|   id="G4e04cb352708f"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G4e04cb352708f"  class=" tableEdit Genetic_interaction_table dataTable"   
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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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{|   id="X46aa060583baa"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46aa060583baa"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTGCCCGCGCGTTAACTCCCG  
Primer 2:CCTTGCCCGCGCGTTAACTCCCG  
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[[:Category:Kohara_Phage:12D1|12D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=637 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:3F12|3F12]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=638 Genobase]
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PMID:3038334
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{|   id="K46aa0606332f7"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46aa0606332f7"  class=" tableEdit Gene_accessions_table"   
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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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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11938 EcoCyc:EG11938]
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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=EB1882 EchoBASE:EB1882]
EcoCyc:EG11938
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b4061 EcoliGenExpDB:b4061]
EcoGene:EG11938
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C5052 ECOL199310CYC:C5052]
RegulonDB:ECK120001866
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11938 EcoGene:EG11938]
[http://www.ncbi.nlm.nih.gov/gene?term=948568 GeneID:948568]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YJCC ECOO157CYC:YJCC]
EchoBASE:EB1882
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0013309&formSubmitReturn=1 ASAP:ABE-0013309]
ASAP:ABE-0013309
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:51, 19 September 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

yjcC

Mnemonic

Systematic nomenclature

Synonyms

ECK4053, b4061, JW4022[1], JW4022

edit table


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

92.11 minutes 

MG1655: 4273494..4275080
<gbrowseImage> name=NC_000913:4273494..4275080 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 4212339..4213925
<gbrowseImage> name=NC_012759:4212339..4213925 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4279061..4280647
<gbrowseImage> name=NC_007779:4279061..4280647 source=W3110 preset=GeneLocation </gbrowseImage>

edit table


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
edit table


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

Strain DH10B

G416C

Nonsynonomous mutation

PMID:18245285[2]

ASAP

This is a SNP in E. coli K-12 Strain DH10B

ΔyjcC (Keio:JW4022)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10890[4]

ΔyjcC755::kan

PMID:16738554[3]

CGSC:105474

yjcC755(del)::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[5]

Parental Strain: SMR4562

Experimental Strain: SMR12056

Mutation was comparatively weak with decrease only happening to 33-67% of population.

yicC750::FRTKanFRT

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[5]

Parental Strain: SMR4562

Experimental Strain: SMR11978

Mutation was comparatively weak with decrease only happening to 33-67% of population.

yjcC755(del)::FRTKanFRT

Sensitivity to

An increase in UV Sensitivity

PMID:23224554[5]

Parental Strain: SMR4562

Experimental Strain: SMR12056

supplemental Table S7 & S1

edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


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

JW4022

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAGTCATCGTGCACGACACCA

Primer 2:CCTTGCCCGCGCGTTAACTCCCG

12D1

Kohara Phage

Genobase

PMID:3038334[7]

3F12

Kohara Phage

Genobase

PMID:3038334[7]

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[4]

est. P1 cotransduction: 27% [8]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[4]

est. P1 cotransduction: 28% [8]

edit table


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:EG11938

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11938

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001866

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948568

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1882

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0013309

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. ↑ Durfee, T et al. (2008) The complete genome sequence of Escherichia coli DH10B: insights into the biology of a laboratory workhorse. J. Bacteriol. 190 2597-606 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 5.2 Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  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).

Categories

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