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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{|   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
|-
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|
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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)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2921543|2923276|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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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]]
|
 
|
DH10B: 3129998..3128265<br /><gbrowseImage>
name=NC_010473:3128265..3129998
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3034029..3037762 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3124799|3133464|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3035029..3036762&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3124799|3133464|FASTA Dump}}
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===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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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="U46a9e8b65428d"  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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|
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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]]
|-
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[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]]
|-  
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|
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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.   
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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
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None
None
|
|
 
|
|
Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation
Reduces expression of recJ gene, can be suppressed by mutations in initiation factor IF3 for translation
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|
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|
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''recJ284::Tn10''
''recJ284''::Tn''10'' (KD2238)
|
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|
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Resistant to
|
|
 
Mutation increases resistance to Thymineless Death (TLD). Figure 1.
|
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PMID:2848620
|
|
[[cgscmutation:72003|CGSC:72003]]
[[cgscmutation:72003|CGSC:72003]]
|
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Parent Strain: KD2197
|-  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[[cgscmutation:102628|CGSC:102628]]
[[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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!|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
!|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
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=469 Genobase]
|
PMID:3038334
|-  
|
|
[[recD:Gene|recD1901::Tn10]]
[[recD:Gene|recD1901::Tn10]]
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|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
|-
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|
|
[[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]]
|-
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0823 EchoBASE:EB0823] 
EcoGene:EG10830
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|
''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=b2892 EcoliGenExpDB:b2892] 
RegulonDB:ECK120000821
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
|
[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=C3472 ECOL199310CYC:C3472]
[http://www.ncbi.nlm.nih.gov/gene?term=947367 GeneID:947367]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10830 EcoGene:EG10830] 
EchoBASE:EB0823
|
|
''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=RECJ ECOO157CYC:RECJ] 
ASAP:ABE-0009492
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
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===Categories===
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[[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: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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