recC: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="F46a9e719ec5f5"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''recC''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''recC''
Recombination
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2818, b2822, JW2790''<ref name='LIB:Riley_2006'/>, JW2790''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16211.F46a9e719ec5f5&page=16211&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2818, b2822, JW2790''<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="R46a9e71a76b06"  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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63.73 minutes&nbsp;
63.73 minutes&nbsp;
|
|
MG1655: 2960450..2957082<br />{{GBrowseFigureByCoord|2956082|2961450|ecoli|MG1655}}
MG1655: 2960450..2957082<br /><gbrowseImage>
name=NC_000913:2957082..2960450
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10825 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10825 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2956082..2961450 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2956082|2961450|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2957082..2960450&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2957082|2960450|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10825 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10825 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2857047..2853679<br /><gbrowseImage>
name=NC_012967:2853679..2857047
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2853679|2857047|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2853679|2857047|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2844230..2847598<br /><gbrowseImage>
name=NC_012759:2844230..2847598
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2844230|2847598|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2844230|2847598|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2961084..2957716<br />{{GBrowseFigureByCoord|2956716|2962084|ecoli_W3110|W3110}}
W3110: 2961084..2957716<br /><gbrowseImage>
name=NC_007779:2957716..2961084
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2956716..2962084 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2956716|2962084|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2957716..2961084&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2957716|2961084|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3054320..3050952<br /><gbrowseImage>
name=NC_010473:3050952..3054320
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3044216|3061056|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3044216|3061056|FASTA Dump}}
 
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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="W46a9e71b33111"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
2957082
|
Edman degradation
|
PMID:3520484<br />
|
 
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<protect><!--Sequence_notes--></protect>
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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="Q46a9e71b7a05f"  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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&Delta;recC (Keio:JW2790)
''recC(del)'' (Keio:JW2790)
|
|
deletion
deletion
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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]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
Line 162: Line 239:


|
|
[[PMID:350827]]<ref name=PMID:350827/>
PMID:350827
|
|
[[cgscmutation:4678|CGSC:4678]]
[[cgscmutation:4678|CGSC:4678]]
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|
|
[[PMID:350827]]<ref name=PMID:350827/>
PMID:350827
|
|
[[cgscmutation:10532|CGSC:10532]]
[[cgscmutation:10532|CGSC:10532]]
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|-
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''recC1003(Chi<sup>-</sup>)''
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|
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|
[[cgscmutation:10536|CGSC:10536]]
|
|-
|
''recC1004(Chi<sup>-</sup>)''
|
|
|
|
|
|
[[cgscmutation:10539|CGSC:10539]]
|
|-
|
''recC1001(Chi<sup>-</sup>)''
|
|
|
|
|
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[[cgscmutation:10540|CGSC:10540]]
|
|-
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''recC23''
|
|
|
|
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[[cgscmutation:16759|CGSC:16759]]
|
|-
|
recC
|
deletion
|
|
Sensitivity to
|
decreases sensitivity to [[Bicyclomycin]]
|
PMID:21357484
|
|
fig 2
|-
|
SMR6039 ''recC''::Tn10DCam
|
Insertion
|
|
SOS-Induction
|
Decrease in spontaneous SOS-Induction
|
PMID:23224554
|
Parent Strain: SMR11941
Experimental Strain: SMR17043
|
The mutation conferred a decrease in spontaneous SOS-induction. See table S7 for a summary of results. 


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW2790
JW2790
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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]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCTGACTGATTAAAGCGAAACAG  
Primer 2:CCTGACTGATTAAAGCGAAACAG  
|-
|-
|
[[:Category:Kohara_Phage:3G11|3G11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=460 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5A10|5A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=461 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: 81% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 81% <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: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <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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|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10825 EcoCyc:EG10825] 
EcoCyc:EG10825
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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=EB0818 EchoBASE:EB0818] 
EcoGene:EG10825
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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=b2822 EcoliGenExpDB:b2822] 
RegulonDB:ECK120000816
|
|
''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=C3416 ECOL199310CYC:C3416]
[http://www.ncbi.nlm.nih.gov/gene?term=947294 GeneID:947294]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10825 EcoGene:EG10825] 
EchoBASE:EB0818
|
|
''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=RECC ECOO157CYC:RECC] 
ASAP:ABE-0009255
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
|
|- class="tableEdit_footer"
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16211.F46a9e71cce5da&page=16211&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/310 CGSC:310] 
|
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===Notes===
===Notes===
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===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: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

recC

Mnemonic

Recombination

Synonyms

ECK2818, b2822, JW2790[1], JW2790

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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

63.73 minutes 

MG1655: 2960450..2957082
<gbrowseImage> name=NC_000913:2957082..2960450 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2857047..2853679
<gbrowseImage> name=NC_012967:2853679..2857047 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2844230..2847598
<gbrowseImage> name=NC_012759:2844230..2847598 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2961084..2957716
<gbrowseImage> name=NC_007779:2957716..2961084 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3054320..3050952
<gbrowseImage> name=NC_010473:3050952..3054320 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

Coding Start (SO:0000323)

MG1655

2957082

Edman degradation

PMID:3520484[2]


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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

recC(del) (Keio:JW2790)

deletion

deletion

PMID:16738554[3]

Shigen

recC22

PMID:350827[4]

CGSC:4678

recC1010(Nuc-)

ds DNA exonuclease-minus

CGSC:10512

recC73

PMID:350827[4]

CGSC:10532

recC1002(Chi-)

CGSC:10534

recC1003(Chi-)

CGSC:10536

recC1004(Chi-)

CGSC:10539

recC1001(Chi-)

CGSC:10540

recC23

CGSC:16759

recC

deletion

Sensitivity to

decreases sensitivity to Bicyclomycin

PMID:21357484[5]

fig 2

SMR6039 recC::Tn10DCam

Insertion

SOS-Induction

Decrease in spontaneous SOS-Induction

PMID:23224554[6]

Parent Strain: SMR11941 Experimental Strain: SMR17043

The mutation conferred a decrease in spontaneous SOS-induction. See table S7 for a summary of results.

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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

JW2790

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCTTAAGGGTCTACCATTCCAA

Primer 2:CCTGACTGATTAAAGCGAAACAG

3G11

Kohara Phage

Genobase

PMID:3038334[8]

5A10

Kohara Phage

Genobase

PMID:3038334[8]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[9]

est. P1 cotransduction: 81% [10]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[9]

est. P1 cotransduction: % [10]
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:EG10825

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10825

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000816

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947294

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0818

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009255

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. ↑ Finch, PW et al. (1986) Complete nucleotide sequence of the Escherichia coli recC gene and of the thyA-recC intergenic region. Nucleic Acids Res. 14 4437-51 PubMed
  3. ↑ 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 Templin, A et al. (1978) Suppressibility of recA, recB, and recC mutations by nonsense suppressors. J. Bacteriol. 134 590-6 PubMed
  5. ↑ 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
  6. ↑ 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
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 CGSC: The Coli Genetics Stock Center
  10. ↑ 10.0 10.1 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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