rppH:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|nudH}}{{Tab On|Gene|nudH}}{{Tab|Gene Product(s)|nudH}}{{Tab|Expression|nudH}}{{Tab|Evolution|nudH}}{{Tab|On One Page|nudH}}{{TabsBottom}}
{{Tab|Quickview|rppH}}{{Tab On|Gene|rppH}}{{Tab|Gene Product(s)|rppH}}{{Tab|Expression|rppH}}{{Tab|Evolution|rppH}}{{Tab|On One Page|rppH}}{{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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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''nudH''  
''rppH <ref name=PMID:18202662/>''
|-
!align=left {{table_heading_style}} |Mnemonic
||
RNA pyrophosphohydrolase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''nudH, ECK2826, b2830, JW2798, ydgP, ygdP''<ref name='LIB:Riley_2006'/>, ygdP''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16227.K46a9e74cf38af&page=16227&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2826, b2830, JW2798, ydgP, ygdP''<ref name='LIB:Riley_2006'/>
|-
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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="Q46a9e74d7ea68"  class=" tableEdit Gene_location_table sortable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 2853617..2854147<br /><gbrowseImage>
name=NC_012759:2853617..2854147
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2853617|2854147|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2853617|2854147|FASTA Dump}}
|-  
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MG1655
MG1655
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63.94 minutes&nbsp;
63.94 minutes&nbsp;
|
|
MG1655: 2966999..2966469<br />{{GBrowseFigureByCoord|2965469|2967999|ecoli|MG1655}}
MG1655: 2966999..2966469<br /><gbrowseImage>
name=NC_000913:2966469..2966999
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7459 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7459 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2965469..2967999 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2965469|2967999|GBrowse(MG1655)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2966469..2966999&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2966469|2966999|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7459 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7459 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2967633..2967103<br />{{GBrowseFigureByCoord|2966103|2968633|ecoli_W3110|W3110}}
W3110: 2967633..2967103<br /><gbrowseImage>
name=NC_007779:2967103..2967633
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2966103..2968633 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2966103|2968633|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2967103..2967633&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2967103|2967633|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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====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="E46a9e74e81e8b"  class=" tableEdit Gene_allele_table sortable dataTable" 
|- {{table_heading_style}}
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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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rppHE53A
|
 
|
E53A
|
 
|
Loss of function
|
 
|
 
|
seeded from [http://www.uniprot.org/uniprot/P0A776 UniProt:P0A776]
|-
|
''nudH(del)'' (Keio:JW2798)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108466 CGSC10185]<ref name='LIB:cgsc'/>
|
|-
|
''rppH5::FLKP2(lacZ,kan)''
|
 
|
 
|
 
|
 
|
PMID:12142427
|
[[cgscmutation:87288|CGSC:87288]]
|
|-
|
''rppH6(del)''
|
 
|
 
|
 
|
 
|
PMID:12142427
|
[[cgscmutation:87291|CGSC:87291]]
|
|-
|
''rppH754(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102140|CGSC:102140]]
|
|-
|
''rppH754(del)''::FRT
|
Deletion
|
 
|
Mutagenesis rate
|
Decrease in Stressed Induced Mutagenesis (SIM).
|
PMID:23224554
|
Parental Strain: SMR4563
Experimental Strain: SMR12210
|
The mutation conferred a decrease in SIM with mutant frequency being reduced by over 90 percent. See table S3. 
|-
|
''rppH754(del)''::FRT
|
Deletion
|
 
|
Sensitivity to
|
SDS-EDTA sensitivity.
|
PMID:23224554
|
Parental Strain: SMR4563
Experimental Strain: SMR12210
|
The mutation conferred a increase in SDS-EDTA sensitivity. See table S7 and S1 for full experimental results. 
|-
|
CAG45114 ''rppH754(del)''::FRTKanFRT
|
Deletion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in Sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45115
Experimental Strain: SMR15315
|
See table S11 for full experimental data. 
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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|- {{table_heading_style}}
!|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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JW2798
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCATTGATGACGATGGCTACCG
 
Primer 2:CCACCTCTTTTACGTCGATAAGC
|-
|
[[recD:Gene|recD1901::Tn10]]
|
Linked marker
|
CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 57% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[speA:Gene|speA210::Tn10]]
|
Linked marker
|
CAG12168 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40110 CGSC7431]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
 
Synonyms:zgd-210::Tn10, zgf-210::Tn10
 
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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=G7459 EcoCyc:G7459] 
EcoCyc:G7459
|
|
''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=EB2896 EchoBASE:EB2896] 
EcoGene:EG13091
|
|
''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=b2830 EcoliGenExpDB:b2830] 
RegulonDB:ECK120004022
|
|
''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=C3425 ECOL199310CYC:C3425]
[http://www.ncbi.nlm.nih.gov/gene?term=947300 GeneID:947300]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13091 EcoGene:EG13091] 
EchoBASE:EB2896
|
|
''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=YGDP ECOO157CYC:YGDP] 
ASAP:ABE-0009276
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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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:rpp genes]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:36, 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

rppH [1]

Mnemonic

RNA pyrophosphohydrolase

Synonyms

nudH, ECK2826, b2830, JW2798, ydgP, ygdP[2], ygdP

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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

BW2952

NC_012759: 2853617..2854147
<gbrowseImage> name=NC_012759:2853617..2854147 source=BW2952 preset=GeneLocation </gbrowseImage>

MG1655

63.94 minutes 

MG1655: 2966999..2966469
<gbrowseImage> name=NC_000913:2966469..2966999 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2967633..2967103
<gbrowseImage> name=NC_007779:2967103..2967633 source=W3110 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

rppHE53A

E53A

Loss of function

seeded from UniProt:P0A776

nudH(del) (Keio:JW2798)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10185[4]

rppH5::FLKP2(lacZ,kan)

PMID:12142427[5]

CGSC:87288

rppH6(del)

PMID:12142427[5]

CGSC:87291

rppH754(del)::kan

PMID:16738554[3]

CGSC:102140

rppH754(del)::FRT

Deletion

Mutagenesis rate

Decrease in Stressed Induced Mutagenesis (SIM).

PMID:23224554[6]

Parental Strain: SMR4563 Experimental Strain: SMR12210

The mutation conferred a decrease in SIM with mutant frequency being reduced by over 90 percent. See table S3.

rppH754(del)::FRT

Deletion

Sensitivity to

SDS-EDTA sensitivity.

PMID:23224554[6]

Parental Strain: SMR4563 Experimental Strain: SMR12210

The mutation conferred a increase in SDS-EDTA sensitivity. See table S7 and S1 for full experimental results.

CAG45114 rppH754(del)::FRTKanFRT

Deletion

SigmaE activity

Decrease in SigmaE activity

PMID:23224554[6]

Parental Strain: CAG45115 Experimental Strain: SMR15315

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

JW2798

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCATTGATGACGATGGCTACCG

Primer 2:CCACCTCTTTTACGTCGATAAGC

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[4]

est. P1 cotransduction: 57% [8]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[4]

est. P1 cotransduction: % [8]

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:G7459

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13091

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004022

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947300

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2896

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009276

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. ↑ Deana, A et al. (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5' pyrophosphate removal. Nature 451 355-8 PubMed
  2. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 Merlin, C et al. (2002) Tools for characterization of Escherichia coli genes of unknown function. J. Bacteriol. 184 4573-81 PubMed
  6. ↑ 6.0 6.1 6.2 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 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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