recJ: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="T46a9e8b4c56b5"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''recJ''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''recJ''
Recombination
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2887, b2892, JW2860''<ref name='LIB:Riley_2006'/>, JW2860''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16349.T46a9e8b4c56b5&page=16349&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2887, b2892, JW2860''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='142244'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Q46a9e8b550bcc"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
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65.4 minutes&nbsp;
65.4 minutes&nbsp;
|
|
MG1655: 3036128..3034395<br />{{GBrowseFigureByCoord|3033395|3037128|ecoli|MG1655}}
MG1655: 3036128..3034395<br /><gbrowseImage>
name=NC_000913:3034395..3036128
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10830 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10830 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3033395..3037128 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3033395|3037128|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3034395..3036128&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3034395|3036128|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10830 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10830 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2923859..2922126<br /><gbrowseImage>
name=NC_012967:2922126..2923859
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2922126|2923859|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2922126|2923859|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2921543..2923276<br /><gbrowseImage>
name=NC_012759:2921543..2923276
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2921543|2923276|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2921543|2923276|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3036762..3035029<br />{{GBrowseFigureByCoord|3034029|3037762|ecoli_W3110|W3110}}  
W3110: 3036762..3035029<br /><gbrowseImage>
name=NC_007779:3035029..3036762
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3034029|3037762|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|3035029|3036762|FASTA Dump}}  
|-
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[[DH10B]]
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3034029..3037762 GBrowse(W3110)]
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3035029..3036762&plugin_action=Go FASTA Dump]
DH10B: 3129998..3128265<br /><gbrowseImage>
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3124799|3133464|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3124799|3133464|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====
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{|class = 'sortable' {{Prettytable}} id='142246'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9e8b65428d"  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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&Delta;recJ (Keio:JW2860)
&Delta;recJ (Keio:JW2860)
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108498 CGSC10217]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108498 CGSC10217]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|-
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009492 recJ::Tn5KAN-I-SceI] (FB20963)
|
Insertion at nt 1026 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20963]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009492 recJ::Tn5KAN-I-SceI] (FB20964)
|
Insertion at nt 1026 in Minus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20964]
|
does not contain [[pKD46]]
|-  
|
|
recJ284::Tn10
recJ284::Tn10
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truncation
truncation
|
|
 
|
|
null phenotype, recombination deficient and UV-sensitive in recBC sbcA and recBC sbcBC backgrounds.  Highly synergistic for UV-sensitivity, recombination deficiency and partial inviability with recBC.   
null phenotype, recombination deficient and UV-sensitive in recBC sbcA and recBC sbcBC backgrounds.  Highly synergistic for UV-sensitivity, recombination deficiency and partial inviability with recBC.   
Line 167: Line 265:
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|-
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recJ77
recJ77
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G to D amino acid 78
G to D amino acid 78
|
|
 
|
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similar to recJ284, null
similar to recJ284, null
|
|
<ref name= 'PMID:6317649'/>
<ref name= 'PMID:6317649'/>
<ref name= 'PMID:625764'/>
<ref name= 'PMID:6257642'/>
|
|


|
|
   
   
|-
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recJ153
recJ153
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None
None
|
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Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation
|
<ref name= 'PMID:4587405'/>
<ref name = 'PMID:6317649'/>
<ref name= 'PMID:9352920'/>
|
|
|
   
   
|-
|
|
|
|
|
Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation
 
|
|
<ref name 'PMID=4587405'/>
 
<ref name 'PMID=6317649'/>
|
<ref name 'PMID=9352920'/>
 
|
|


|
|
   
   
|-
|-  
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''recJ153''
|
 
|
 
|
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|
[[cgscmutation:7801|CGSC:7801]]
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|-
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''recJ284''::Tn''10'' (KD2238)
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|


|
|


|
Resistant to
|
Mutation increases resistance to Thymineless Death (TLD). Figure 1.
|
PMID:2848620
|
[[cgscmutation:72003|CGSC:72003]]
|
Parent Strain: KD2197
|-
|
''&#916;recJ743::kan''
|
|


|
|
|
|
PMID:16738554
|
[[cgscmutation:102628|CGSC:102628]]
|
|
   
   
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N4e04c22cf39a1"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
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JW2860
JW2860
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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:CCAATTGGCCAGATATTGTCGAT  
Primer 2:CCAATTGGCCAGATATTGTCGAT  
|-
|-
|
[[:Category:Kohara_Phage:5B4|5B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=467 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:22H4|22H4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=468 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5E11|5E11]]
|
Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=469 Genobase]
|
PMID:3038334
|-  
|
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[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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|
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[speA:Gene|speA210::Tn10]]
[[speA:Gene|speA210::Tn10]]
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CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zgd-210::Tn10, zgf-210::Tn10


Synonyms:zgd-210::Tn10, zgf-210::Tn10
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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]]
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|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10830 EcoCyc:EG10830] 
EcoCyc:EG10830
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|-  
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0823 EchoBASE:EB0823] 
|
|-
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2892 EcoliGenExpDB:b2892] 
EcoGene:EG10830
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3472 ECOL199310CYC:C3472] 
RegulonDB:ECK120000821
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10830 EcoGene:EG10830]
[http://www.ncbi.nlm.nih.gov/gene?term=947367 GeneID:947367]
|
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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=RECJ ECOO157CYC:RECJ] 
EchoBASE:EB0823
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/17965 CGSC:17965] 
ASAP:ABE-0009492
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
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[[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:rec genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

recJ

Mnemonic

Recombination

Synonyms

ECK2887, b2892, JW2860[1], JW2860

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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

65.4 minutes 

MG1655: 3036128..3034395
<gbrowseImage> name=NC_000913:3034395..3036128 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2923859..2922126
<gbrowseImage> name=NC_012967:2922126..2923859 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2921543..2923276
<gbrowseImage> name=NC_012759:2921543..2923276 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3036762..3035029
<gbrowseImage> name=NC_007779:3035029..3036762 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3129998..3128265
<gbrowseImage> name=NC_010473:3128265..3129998 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

ΔrecJ (Keio:JW2860)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10217[3]

recJ::Tn5KAN-I-SceI (FB20963)

Insertion at nt 1026 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20963

contains pKD46

recJ::Tn5KAN-I-SceI (FB20964)

Insertion at nt 1026 in Minus orientation

PMID:15262929[4]

E. coli Genome Project:FB20964

does not contain pKD46

recJ284::Tn10

Insertion of Tn10 (Tetracycline-resistance) at nucleotide 434 relative to GTG start codon

truncation

null phenotype, recombination deficient and UV-sensitive in recBC sbcA and recBC sbcBC backgrounds. Highly synergistic for UV-sensitivity, recombination deficiency and partial inviability with recBC.

[5]

CGSC

recJ77

G to A nucleotide 281

G to D amino acid 78

similar to recJ284, null

[5] [6]

recJ153 recJ154

GTG to GTA at start codon

None

Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation

[7] [5] [8]

recJ153

CGSC:7801

recJ284::Tn10 (KD2238)

Resistant to

Mutation increases resistance to Thymineless Death (TLD). Figure 1.

PMID:2848620[9]

CGSC:72003

Parent Strain: KD2197

ΔrecJ743::kan

PMID:16738554[2]

CGSC:102628


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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

JW2860

Plasmid clone

Shigen

PMID:16769691[10]

Status:Clone OK

Primer 1:GCCAAACAACAGATACAACTTCG

Primer 2:CCAATTGGCCAGATATTGTCGAT

5B4

Kohara Phage

Genobase

PMID:3038334[11]

22H4

Kohara Phage

Genobase

PMID:3038334[11]

5E11

Kohara Phage

Genobase

PMID:3038334[11]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: % [12]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: 9% [12]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10830

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10830

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000821

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947367

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0823

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009492

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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ 5.0 5.1 5.2 Lovett, ST & Clark, AJ (1984) Genetic analysis of the recJ gene of Escherichia coli K-12. J. Bacteriol. 157 190-6 PubMed
  6. ↑ Gillen, JR et al. (1981) Genetic analysis of the RecE pathway of genetic recombination in Escherichia coli K-12. J. Bacteriol. 145 521-32 PubMed
  7. ↑ Horii, Z & Clark, AJ (1973) Genetic analysis of the recF pathway to genetic recombination in Escherichia coli K12: isolation and characterization of mutants. J. Mol. Biol. 80 327-44 PubMed
  8. ↑ Haggerty, TJ & Lovett, ST (1997) IF3-mediated suppression of a GUA initiation codon mutation in the recJ gene of Escherichia coli. J. Bacteriol. 179 6705-13 PubMed
  9. ↑ Nakayama, K et al. (1988) Thymineless death in Escherichia coli mutants deficient in the RecF recombination pathway. Can. J. Microbiol. 34 905-7 PubMed
  10. ↑ 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
  11. ↑ 11.0 11.1 11.2 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
  12. ↑ 12.0 12.1 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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