recF:Gene: Difference between revisions

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{{Tab|Quickview|recF}}{{Tab On|Gene|recF}}{{Tab|Gene Product(s)|recF}}{{Tab|Expression|recF}}{{Tab|Evolution|recF}}{{Tab|On One Page|recF}}{{TabsBottom}}
{{Tab|Quickview|recF}}{{Tab On|Gene|recF}}{{Tab|Gene Product(s)|recF}}{{Tab|Expression|recF}}{{Tab|Evolution|recF}}{{Tab|On One Page|recF}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''recF''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''recF''
Recombination
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3692, b3700, JW3677, uvrF''<ref name='LIB:Riley_2006'/>, uvrF''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17959.V46a9fca6b9082&page=17959&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3692, b3700, JW3677, uvrF''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X46a9fca747553"  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
|-
|-  
|
|
MG1655
MG1655
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83.59 minutes, 83.59 minutes&nbsp;
83.59 minutes, 83.59 minutes&nbsp;
|
|
MG1655: 3879244..3878171<br />{{GBrowseFigureByCoord|3877171|3880244|ecoli|MG1655}}
MG1655: 3879244..3878171<br /><gbrowseImage>
name=NC_000913:3878171..3879244
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10828 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10828 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3877171..3880244 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3877171|3880244|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3878171..3879244&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3878171|3879244|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10828 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10828 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3841582..3840509<br /><gbrowseImage>
name=NC_012967:3840509..3841582
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3840509|3841582|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3840509|3841582|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3766504..3767577<br /><gbrowseImage>
name=NC_012759:3766504..3767577
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3766504|3767577|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3766504|3767577|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3759194..3760267<br />{{GBrowseFigureByCoord|3758194|3761267|ecoli_W3110|W3110}}  
W3110: 3759194..3760267<br /><gbrowseImage>
name=NC_007779:3759194..3760267
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3758194|3761267|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3758194..3761267 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|3759194|3760267|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3759194..3760267&plugin_action=Go FASTA Dump]
[[DH10B]]
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|
DH10B: 3976828..3975755<br /><gbrowseImage>
name=NC_010473:3975755..3976828
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3973609|3978974|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3973609|3978974|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9fca811245"  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
|-class='sortbottom'
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Coding Start (SO:0000323)
|
[[MG1655]]
|
3878174
|
Edman degradation
|
PMID:2228960<br />
|
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9fca85b470"  class=" tableEdit Gene_allele_table dataTable" 
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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recF(del) (Keio:JW3677)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012095 recF::Tn5KAN-I-SceI] (FB21402)
|
Insertion at nt 370 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21402]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0012095 recF::Tn5KAN-I-SceI] (FB21403)
|
Insertion at nt 370 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB21403]
|
contains [[pKD46]]
|-
|
recFK36R
|
 
|
K36R
|
 
|
Weakly active
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A7H0 UniProt:P0A7H0]
|-
|
''recF143''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:10318|CGSC:10318]]
|
|-
|
''recF400::Tn5''
|
 
|
 
|
 
|
 
|
PMID:2841294
|
[[cgscmutation:67402|CGSC:67402]]
|
|-
|
recF
|
deletion
|
 
|
Sensitivity to
|
decreases sensitivity to [[Bicyclomycin]]
|
PMID:21357484
|
 
|
fig 2
|-
|
''recF349''
|
 
|
 
|
Growth Phenotype
|
Mutations show approximately 50% decrease in viability relative to the wild type, table 1.
|
PMID:8820655
|
JC18536
|
|-
|
''recF4101'' ''priA2:kan''
|
 
|
 
|
Growth Phenotype
|
Double mutation decreases cell viability from wildtype, table 1.
|
PMID:8820655
|
experimental strain: JC18991
|
|-
|
''recF4115'' ''priA2:kan''
|
 
|
 
|
Growth Phenotype
|
Double mutation decreases cell viability, table 1.
|
PMID:8820655
|
JC18996
|
|-
|
''recF143'' ''priA2::kan''
|
 
|
 
|
Growth Phenotype
|
Double mutation causes decreased cell viability, table 1.
|
PMID:8820655
|
JC18989
|
|-
|
''recF143''
|
 
|
 
|
Sensitivity to
|
mutant shows attenuated UV-inducible SOS expression compared to wildtype, fig 1B.
|
PMID:8820655
|
 
|
 
|- class="tableEdit_footer"
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.17959.F4e04c22a90e75-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F4e04c22a90e75"  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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|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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JW3677
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCTCCCTCACCCGCTTGTTGAT
 
Primer 2:CCATCCGTTATTTTACCCTTTTC
|-
|
[[:Category:Kohara_Phage:3C10|3C10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=565 Genobase]
|
PMID:3038334
|-
|
zid-501::Tn10
|
Linked marker
|
CAG18499 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38945 CGSC7458]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[rbsA:Gene|rbsD296::Tn10]]
|
Linked marker
|
CAG18501 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40333 CGSC7460]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zie-296::Tn10
 
|- class="tableEdit_footer"
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10828 EcoCyc:EG10828] 
EcoCyc:EG10828
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0821 EchoBASE:EB0821] 
EcoGene:EG10828
|
|
''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=b3700 EcoliGenExpDB:b3700] 
RegulonDB:ECK120000819
|
|
''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=C4622 ECOL199310CYC:C4622]
[http://www.ncbi.nlm.nih.gov/gene?term=948209 GeneID:948209]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10828 EcoGene:EG10828] 
EchoBASE:EB0821
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=RECF ECOO157CYC:RECF] 
ASAP:ABE-0012095
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout 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 20:49, 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

recF

Mnemonic

Recombination

Synonyms

ECK3692, b3700, JW3677, uvrF[1], uvrF

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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

83.59 minutes, 83.59 minutes 

MG1655: 3879244..3878171
<gbrowseImage> name=NC_000913:3878171..3879244 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3841582..3840509
<gbrowseImage> name=NC_012967:3840509..3841582 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3766504..3767577
<gbrowseImage> name=NC_012759:3766504..3767577 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3759194..3760267
<gbrowseImage> name=NC_007779:3759194..3760267 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3976828..3975755
<gbrowseImage> name=NC_010473:3975755..3976828 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

3878174

Edman degradation

PMID:2228960[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

recF(del) (Keio:JW3677)

deletion

deletion

PMID:16738554[3]

Shigen

recF::Tn5KAN-I-SceI (FB21402)

Insertion at nt 370 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21402

does not contain pKD46

recF::Tn5KAN-I-SceI (FB21403)

Insertion at nt 370 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21403

contains pKD46

recFK36R

K36R

Weakly active

seeded from UniProt:P0A7H0

recF143

CGSC:10318

recF400::Tn5

PMID:2841294[5]

CGSC:67402

recF

deletion

Sensitivity to

decreases sensitivity to Bicyclomycin

PMID:21357484[6]

fig 2

recF349

Growth Phenotype

Mutations show approximately 50% decrease in viability relative to the wild type, table 1.

PMID:8820655[7]

JC18536

recF4101 priA2:kan

Growth Phenotype

Double mutation decreases cell viability from wildtype, table 1.

PMID:8820655[7]

experimental strain: JC18991

recF4115 priA2:kan

Growth Phenotype

Double mutation decreases cell viability, table 1.

PMID:8820655[7]

JC18996

recF143 priA2::kan

Growth Phenotype

Double mutation causes decreased cell viability, table 1.

PMID:8820655[7]

JC18989

recF143

Sensitivity to

mutant shows attenuated UV-inducible SOS expression compared to wildtype, fig 1B.

PMID:8820655[7]


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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

JW3677

Plasmid clone

Shigen

PMID:16769691[8]

Status:Clone OK

Primer 1:GCCTCCCTCACCCGCTTGTTGAT

Primer 2:CCATCCGTTATTTTACCCTTTTC

3C10

Kohara Phage

Genobase

PMID:3038334[9]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[10]

est. P1 cotransduction: 87% [11]

rbsD296::Tn10

Linked marker

CAG18501 = CGSC7460[10]

est. P1 cotransduction: 9% [11]
Synonyms:zie-296::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:EG10828

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10828

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000819

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948209

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0821

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012095

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. ↑ Griffin, TJ 4th & Kolodner, RD (1990) Purification and preliminary characterization of the Escherichia coli K-12 recF protein. J. Bacteriol. 172 6291-9 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 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Thoms, B & Wackernagel, W (1988) Suppression of the UV-sensitive phenotype of Escherichia coli recF mutants by recA(Srf) and recA(Tif) mutations requires recJ+. J. Bacteriol. 170 3675-81 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 7.2 7.3 7.4 Sandler, SJ (1996) Overlapping functions for recF and priA in cell viability and UV-inducible SOS expression are distinguished by dnaC809 in Escherichia coli K-12. Mol. Microbiol. 19 871-80 PubMed
  8. ↑ 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
  9. ↑ 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
  10. ↑ 10.0 10.1 CGSC: The Coli Genetics Stock Center
  11. ↑ 11.0 11.1 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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