rssB:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|rssB}}{{Tab On|Gene|rssB}}{{Tab|Gene Product(s)|rssB}}{{Tab|Expression|rssB}}{{Tab|Evolution|rssB}}{{Tab|On One Page|rssB}}{{TabsBottom}}
{{Tab|Quickview|rssB}}{{Tab On|Gene|rssB}}{{Tab|Gene Product(s)|rssB}}{{Tab|Expression|rssB}}{{Tab|Evolution|rssB}}{{Tab|On One Page|rssB}}{{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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="R46a9c2a483c11"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''rssB''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''rssB''
Regulation of Sigma S
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL''<ref name='LIB:Riley_2006'/>, verA, ychL''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13037.R46a9c2a483c11&page=13037&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="S46a9c2a5096ce"  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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27.79 minutes&nbsp;
27.79 minutes&nbsp;
|
|
MG1655: 1289465..1290478<br />{{GBrowseFigureByCoord|1288465|1291478|ecoli|MG1655}}
MG1655: 1289465..1290478<br /><gbrowseImage>
name=NC_000913:1289465..1290478
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12121 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12121 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1288465..1291478 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1288465|1291478|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1289465..1290478&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1289465|1290478|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12121 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12121 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1290036..1291049<br /><gbrowseImage>
name=NC_012967:1290036..1291049
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1290036|1291049|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1290036|1291049|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 1179050..1179976<br /><gbrowseImage>
name=NC_012759:1179050..1179976
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1179050|1179976|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1179050|1179976|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1291819..1292832<br />{{GBrowseFigureByCoord|1290819|1293832|ecoli_W3110|W3110}}  
W3110: 1291819..1292832<br /><gbrowseImage>
name=NC_007779:1291819..1292832
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1290819|1293832|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1291819|1292832|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1329706..1330719<br /><gbrowseImage>
name=NC_010473:1329706..1330719
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1290819..1293832 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1327680|1332745|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1291819..1292832&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1327680|1332745|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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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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==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="W46a9c2a5ec566"  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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&Delta;rssB (Keio:JW1223)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107390 CGSC9109]<ref name='LIB:cgsc'/>
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|D-Galactoniate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Hydroxybutyrate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketobutyrate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|a-Ketoglutarate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Succinate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Bromosuccinate]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Alanine]]
|
PMID:16095938
|
 
|
|-
|
&Delta;sprE::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|L-Asparagine]]
|
PMID:16095938
|
 
|
|-
|
''&#916;rssB1273''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:77156|CGSC:77156]]
|
|-
|
''&#916;rssB744::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102826|CGSC:102826]]
|
|-
|
overproduction
|
 
|
 
|
Growth Phenotype
|
toxic
|
 
|
 
|
Suppressed by pcnA and hfq mutants PMID:19767441
|-
|
CAG45114 ''rssB''::Tet
|
insertion
|
 
|
Sigma<sup>E</sup> activity
|
Increase in sigma<sup>E</sup> activity
|
PMID:23224554
|
Paternal Strain: CAG45114
Experimental Strain: SMR15271
|
See table S11 for full experimental data. 
 
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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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JW1223
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCACGCAGCCATTGGTCGGAAA
 
Primer 2:CCTTCTGCAGACAACATCAAGCG
|-
|
[[:Category:Kohara_Phage:12H9|12H9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=249 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4D8|4D8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=250 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3D5|3D5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=251 Genobase]
|
PMID:3038334
|-
|
[[fadR:Gene|fadR13::Tn10]]
|
Linked marker
|
CAG18497 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39426 CGSC7365]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 7% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[oppC:Gene|oppC506::Tn10]]
|
Linked marker
|
CAG12169 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38027 CGSC7369]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 61% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zch-506::Tn10, zci-506::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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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=EG12121 EcoCyc:EG12121] 
EcoCyc:EG12121
|
|
''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=EB2042 EchoBASE:EB2042] 
EcoGene:EG12121
|
|
''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=b1235 EcoliGenExpDB:b1235] 
RegulonDB:ECK120002024
|
|
''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]])
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[http://BioCyc.org/ECOL199310/new-image?object=C1699 ECOL199310CYC:C1699]
[http://www.ncbi.nlm.nih.gov/gene?term=945855 GeneID:945855]
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Escherichia coli str. K-12 substr. MG1655
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12121 EcoGene:EG12121]
[[EchoBASE]]
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EchoBASE:EB2042
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://BioCyc.org/ECOO157/new-image?object=HNR ECOO157CYC:HNR]
[[ASAP]]
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ASAP:ABE-0004147
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/37471 CGSC:37471] 
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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:rss genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:30, 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

rssB

Mnemonic

Regulation of Sigma S

Synonyms

ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL[1], verA, ychL

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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

27.79 minutes 

MG1655: 1289465..1290478
<gbrowseImage> name=NC_000913:1289465..1290478 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1290036..1291049
<gbrowseImage> name=NC_012967:1290036..1291049 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1179050..1179976
<gbrowseImage> name=NC_012759:1179050..1179976 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1291819..1292832
<gbrowseImage> name=NC_007779:1291819..1292832 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1329706..1330719
<gbrowseImage> name=NC_010473:1329706..1330719 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

ΔrssB (Keio:JW1223)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9109[3]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire D-Galactoniate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[4]

ΔrssB1273

CGSC:77156

ΔrssB744::kan

PMID:16738554[2]

CGSC:102826

overproduction

Growth Phenotype

toxic

Suppressed by pcnA and hfq mutants PMID:19767441[5]

CAG45114 rssB::Tet

insertion

SigmaE activity

Increase in sigmaE activity

PMID:23224554[6]

Paternal Strain: CAG45114 Experimental Strain: SMR15271

See table S11 for full experimental data.

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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

JW1223

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACGCAGCCATTGGTCGGAAA

Primer 2:CCTTCTGCAGACAACATCAAGCG

12H9

Kohara Phage

Genobase

PMID:3038334[8]

4D8

Kohara Phage

Genobase

PMID:3038334[8]

3D5

Kohara Phage

Genobase

PMID:3038334[8]

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[3]

est. P1 cotransduction: 7% [9]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[3]

est. P1 cotransduction: 61% [9]
Synonyms:zch-506::Tn10, zci-506::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:EG12121

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12121

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002024

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945855

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2042

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004147

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 4.2 4.3 4.4 4.5 4.6 4.7 4.8 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Carabetta, VJ et al. (2009) The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J. Bacteriol. 191 6812-21 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 8.2 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
  9. ↑ 9.0 9.1 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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