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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{| id="F46a9e719ec5f5"  class=" tableEdit Gene_nomenclature_table"   
{|   id="F46a9e719ec5f5"  class=" tableEdit Gene_nomenclature_table"   


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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
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''ECK2818, b2822, JW2790''<ref name='LIB:Riley_2006'/>
''ECK2818, b2822, JW2790''<ref name='LIB:Riley_2006'/>, JW2790''


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****************************************************************************************** -->{{Gene_location_help}}
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{|   id="R46a9e71a76b06"  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="R46a9e71a76b06"  class=" tableEdit Gene_location_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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63.73 minutes&nbsp;
63.73 minutes&nbsp;
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|
MG1655: 2960450..2957082<br />{{GBrowseFigureByCoord|2957082|2960450|ecoli|MG1655}}
MG1655: 2960450..2957082<br /><gbrowseImage>
name=NC_000913:2957082..2960450
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[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]
{{GBrowseLink|ecoli|NC_000913|2956082|2961450|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2956082|2961450|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|2957082|2960450|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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NC_012967: 2857047..2853679<br />{{GBrowseFigureByCoord|2853679|2857047|REL606|NC_012967}}
NC_012967: 2857047..2853679<br /><gbrowseImage>
name=NC_012967:2853679..2857047
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|REL606|NC_012967|2853679|2857047|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|2853679|2857047|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2853679|2857047|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|2853679|2857047|FASTA Dump}}  
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[[BW2952]]
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NC_012759: 2844230..2847598<br /><gbrowseImage>
name=NC_012759:2844230..2847598
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|2844230|2847598|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2844230|2847598|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 2961084..2957716<br />{{GBrowseFigureByCoord|2957716|2961084|ecoli_W3110|W3110}}
W3110: 2961084..2957716<br /><gbrowseImage>
name=NC_007779:2957716..2961084
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|2956716|2962084|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2956716|2962084|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|2957716|2961084|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|2957716|2961084|FASTA Dump}}  
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DH10B: 3054320..3050952<br />{{GBrowseFigureByCoord|3050952|3054320|ecoli_DH10B|DH10B}}
DH10B: 3054320..3050952<br /><gbrowseImage>
name=NC_010473:3050952..3054320
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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{{GBrowseLink|ecoli_DH10B|NC_010473|3044216|3061056|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3044216|3061056|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|3044216|3061056|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|3044216|3061056|FASTA Dump}}  


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{|   id="W46a9e71b33111"  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="W46a9e71b33111"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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{| {{Prettytable}} id="Q46a9e71b7a05f"  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="Q46a9e71b7a05f"  class=" tableEdit Gene_allele_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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)
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deletion
deletion
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recC
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deletion
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Sensitivity to
|
decreases sensitivity to [[Bicyclomycin]]
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PMID:21357484
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fig 2
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SMR6039 ''recC''::Tn10DCam
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Insertion
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SOS-Induction
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Decrease in spontaneous SOS-Induction
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PMID:23224554
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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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04c22730b25"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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{|   id="H46a9e71c35d6b"  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="H46a9e71c35d6b"  class=" tableEdit Gene_resource_table"   
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Primer 2:CCTGACTGATTAAAGCGAAACAG  
Primer 2:CCTGACTGATTAAAGCGAAACAG  
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[[:Category:Kohara_Phage:3G11|3G11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=460 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:5A10|5A10]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=461 Genobase]
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PMID:3038334
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9e71cce5da"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG10825 EcoCyc:EG10825]
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|-
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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=EB0818 EchoBASE:EB0818]
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|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2822 EcoliGenExpDB:b2822]
EcoCyc:EG10825
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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]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C3416 ECOL199310CYC:C3416]
EcoGene:EG10825
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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]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10825 EcoGene:EG10825]
RegulonDB:ECK120000816
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
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[http://BioCyc.org/ECOO157/new-image?object=RECC ECOO157CYC:RECC]
[http://www.ncbi.nlm.nih.gov/gene?term=947294 GeneID:947294]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/310 CGSC:310]
EchoBASE:EB0818
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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=0009255&formSubmitReturn=1 ASAP:ABE-0009255]
ASAP:ABE-0009255
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments

Latest revision as of 20:44, 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

recC

Mnemonic

Recombination

Synonyms

ECK2818, b2822, JW2790[1], JW2790

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

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]


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

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.

edit table


Notes

Genetic Interactions

[back to top]



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


Notes

Genetic Resources

[back to top]


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

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: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

[back to top]



<protect>

References

[back to top]


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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