yjcC:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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{|{{Prettytable}}
{|   id="D46aa0603267e6"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''yjcC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yjcC''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK4053, b4061, JW4022''<ref name='LIB:Riley_2006'/>, JW4022''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18681.D46aa0603267e6&page=18681&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK4053, b4061, JW4022''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===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="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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MG1655
MG1655
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92.11 minutes&nbsp;
92.11 minutes&nbsp;
|
|
MG1655: 4273494..4275080<br />{{GBrowseFigureByCoord|4272494|4276080|ecoli|MG1655}}
MG1655: 4273494..4275080<br /><gbrowseImage>
name=NC_000913:4273494..4275080
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[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]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4272494..4276080 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4272494|4276080|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4273494..4275080&plugin_action=Go 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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[[BW2952]]
|
 
|
NC_012759: 4212339..4213925<br /><gbrowseImage>
name=NC_012759:4212339..4213925
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|4212339|4213925|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|4212339|4213925|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 4279061..4280647<br />{{GBrowseFigureByCoord|4278061|4281647|ecoli_W3110|W3110}}
W3110: 4279061..4280647<br /><gbrowseImage>
name=NC_007779:4279061..4280647
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4278061..4281647 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|4278061|4281647|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4279061..4280647&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4279061|4280647|FASTA Dump}}
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| 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" 
|- {{table_heading_style}}
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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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Strain DH10B
|
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G416C
|
|
Nonsynonomous mutation
|
PMID:18245285
|
[https://asap.ahabs.wisc.edu/asap/home.php ASAP]
|
This is a SNP in <i>E. coli</i> K-12 Strain [[DH10B]]
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109171 CGSC10890]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109171 CGSC10890]<ref name='LIB:cgsc'/>  
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[[cgscmutation:105474|CGSC:105474]]
[[cgscmutation:105474|CGSC:105474]]
|
|
   
   
|-
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''yjcC755(del)''::FRTKanFRT
|
|
|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
Experimental Strain: SMR12056
|
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
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
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
|
Parental Strain: SMR4562
 
Experimental Strain: SMR12056
|
supplemental Table S7 & S1
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW4022
JW4022
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTTGCCCGCGCGTTAACTCCCG  
Primer 2:CCTTGCCCGCGCGTTAACTCCCG  
|-
|-
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[[:Category:Kohara_Phage:12D1|12D1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=637 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3F12|3F12]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=638 Genobase]
|
PMID:3038334
|-  
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[[malF:Gene|malF3089::Tn10]]
[[malF:Gene|malF3089::Tn10]]
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|
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est. P1 cotransduction: 27% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 27% <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
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[[yjcS:Gene|zje-2241::Tn10]]
[[yjcS:Gene|zje-2241::Tn10]]
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|
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est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 28% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11938 EcoCyc:EG11938] 
EcoCyc:EG11938
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1882 EchoBASE:EB1882] 
EcoGene:EG11938
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b4061 EcoliGenExpDB:b4061] 
RegulonDB:ECK120001866
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C5052 ECOL199310CYC:C5052]
[http://www.ncbi.nlm.nih.gov/gene?term=948568 GeneID:948568]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11938 EcoGene:EG11938] 
EchoBASE:EB1882
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YJCC ECOO157CYC:YJCC] 
ASAP:ABE-0013309
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yjc genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:51, 19 September 2013

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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

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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

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>

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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

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

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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

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]

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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: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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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).

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