ubiH:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ubiH}}{{Tab On|Gene|ubiH}}{{Tab|Gene Product(s)|ubiH}}{{Tab|Expression|ubiH}}{{Tab|Evolution|ubiH}}{{Tab|On One Page|ubiH}}{{TabsBottom}}
{{Tab|Quickview|ubiH}}{{Tab On|Gene|ubiH}}{{Tab|Gene Product(s)|ubiH}}{{Tab|Expression|ubiH}}{{Tab|Evolution|ubiH}}{{Tab|On One Page|ubiH}}{{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="M46a9e914500de"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ubiH''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ubiH''
Ubiquinone
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2902, b2907, JW2875, visB, acd''<ref name='LIB:Riley_2006'/>, acd''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.16379.M46a9e914500de&page=16379&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK2902, b2907, JW2875, visB, acd''<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="W46a9e914cf613"  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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65.75 minutes&nbsp;
65.75 minutes&nbsp;
|
|
MG1655: 3051540..3050362<br />{{GBrowseFigureByCoord|3049362|3052540|ecoli|MG1655}}
MG1655: 3051540..3050362<br /><gbrowseImage>
name=NC_000913:3050362..3051540
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11324 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11324 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3049362..3052540 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3049362|3052540|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3050362..3051540&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3050362|3051540|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11324 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11324 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2939269..2938091<br /><gbrowseImage>
name=NC_012967:2938091..2939269
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2938091|2939269|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2938091|2939269|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2937510..2938688<br /><gbrowseImage>
name=NC_012759:2937510..2938688
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2937510|2938688|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2937510|2938688|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3052174..3050996<br />{{GBrowseFigureByCoord|3049996|3053174|ecoli_W3110|W3110}}  
W3110: 3052174..3050996<br /><gbrowseImage>
name=NC_007779:3050996..3052174
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3049996|3053174|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3050996|3052174|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3049996..3053174 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3050996..3052174&plugin_action=Go FASTA Dump]
 
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DH10B: 3145410..3144232<br /><gbrowseImage>
name=NC_010473:3144232..3145410
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3141876|3147766|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3141876|3147766|FASTA Dump}}
 
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<!--Location_notes--></protect>
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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="R46a9e9158bdf0"  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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====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="E46a9e915d335a"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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''ubiH(del)'' (Keio:JW2875)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=108511 CGSC10230]<ref name='LIB:cgsc'/>
|
|-
|
''ubiH101''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:7477|CGSC:7477]]
|
|-
|
''ubiH758(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:103272|CGSC:103272]]
|
|-
|
''visB103''
|
 
|
 
|
Sensitivity to
|
visible light (460nm)
|
PMID:1339425
|
 
|
Strains VS550 and VS551
|-
|
''visB(del)''
|
deletion
|
deletion
|
Sensitivity to
|
visible light (460nm)
|
PMID:1339425
|
 
|
Strain VS560 and VS005
|-
|
''visB(del):KmR ubiA''
|
deletion
|
deletion
|
 
|
not photosensitive
|
PMID:1339425
|
 
|
Strain VS561
|-
|
''ubiH758''(del)::FRT
|
deletion
|
 
|
Mutagenesis Rate
|
Decrease in Stress Induced Mutagenesis (SIM)
|
PMID:23224554
|
Parent Strain: SMR4562
Experimental Strain: SMR12260
|
The mutation caused a strong decrease in the level of SIM, over 90 percent decrease of the Wild Type levels.  See Table S3 for full experimental results. 
|-
|
''ubiH758''(del)::FRT
|
deletion
|
 
|
Sensitivity to
|
Increase in SDS-EDTA sensitivity
|
PMID:23224554
|
Parent Strain: SMR4562
Experimental Strain: SMR12260
|
SDS-EDTA sensitivity increased relative toward the wild type. See table S7 and S1 for a summary of experimental results. 
|-
|
SMR4562 yiaG-yfp FRTcatFRT ''ubiH758(del)''::FRTKanFRT
|
Deletion
|
 
|
Sigma <sup>S</sup> activity
|
Decrease in Sigma<sup>S</sup> activity
|
PMID:23224554
|
Parental Strain: SMR10582
Experimental Strain: SMR12686
|
See table S8 for full experimental strain
|-
|
CAG45114 ''ubiH758(del)''::FRTKanFRT
|
deletion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in Sigma<sup>E</sup> activity
|
PMID:23224554
|
Parental Strain: CAG45114
Experimental Strain: SMR15295
|
See table S11 for full experimental calculations. 
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04c5293e7bb"  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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JW2875
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAGCGTAATCATCGTCGGTGG
 
Primer 2:CCACGCGCCACCCAACCGAGGGT
|-
|
[[:Category:Kohara_Phage:5E11|5E11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=469 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10B4|10B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=470 Genobase]
|
PMID:3038334
|-
|
[[recD:Gene|recD1901::Tn10]]
|
Linked marker
|
CAG12135 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40106 CGSC7429]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <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: 24% <ref name='LIB:Nichols_linked_Tn'/> <br />
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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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11324 EcoCyc:EG11324] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1300 EchoBASE:EB1300] 
EcoCyc:EG11324
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2907 EcoliGenExpDB:b2907] 
EcoGene:EG11324
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3489 ECOL199310CYC:C3489] 
RegulonDB:ECK120001295
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11324 EcoGene:EG11324]
[http://www.ncbi.nlm.nih.gov/gene?term=947388 GeneID:947388]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=UBIH ECOO157CYC:UBIH] 
EchoBASE:EB1300
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/43 CGSC:43] 
ASAP:ABE-0009545
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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:ubi 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

ubiH

Mnemonic

Ubiquinone

Synonyms

ECK2902, b2907, JW2875, visB, acd[1], acd

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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

65.75 minutes 

MG1655: 3051540..3050362
<gbrowseImage> name=NC_000913:3050362..3051540 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2939269..2938091
<gbrowseImage> name=NC_012967:2938091..2939269 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2937510..2938688
<gbrowseImage> name=NC_012759:2937510..2938688 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3052174..3050996
<gbrowseImage> name=NC_007779:3050996..3052174 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3145410..3144232
<gbrowseImage> name=NC_010473:3144232..3145410 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

ubiH(del) (Keio:JW2875)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10230[3]

ubiH101

CGSC:7477

ubiH758(del)::kan

PMID:16738554[2]

CGSC:103272

visB103

Sensitivity to

visible light (460nm)

PMID:1339425[4]

Strains VS550 and VS551

visB(del)

deletion

deletion

Sensitivity to

visible light (460nm)

PMID:1339425[4]

Strain VS560 and VS005

visB(del):KmR ubiA

deletion

deletion

not photosensitive

PMID:1339425[4]

Strain VS561

ubiH758(del)::FRT

deletion

Mutagenesis Rate

Decrease in Stress Induced Mutagenesis (SIM)

PMID:23224554[5]

Parent Strain: SMR4562 Experimental Strain: SMR12260

The mutation caused a strong decrease in the level of SIM, over 90 percent decrease of the Wild Type levels. See Table S3 for full experimental results.

ubiH758(del)::FRT

deletion

Sensitivity to

Increase in SDS-EDTA sensitivity

PMID:23224554[5]

Parent Strain: SMR4562 Experimental Strain: SMR12260

SDS-EDTA sensitivity increased relative toward the wild type. See table S7 and S1 for a summary of experimental results.

SMR4562 yiaG-yfp FRTcatFRT ubiH758(del)::FRTKanFRT

Deletion

Sigma S activity

Decrease in SigmaS activity

PMID:23224554[5]

Parental Strain: SMR10582 Experimental Strain: SMR12686

See table S8 for full experimental strain

CAG45114 ubiH758(del)::FRTKanFRT

deletion

SigmaE activity

Decrease in SigmaE activity

PMID:23224554[5]

Parental Strain: CAG45114 Experimental Strain: SMR15295

See table S11 for full experimental calculations.

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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

JW2875

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAGCGTAATCATCGTCGGTGG

Primer 2:CCACGCGCCACCCAACCGAGGGT

5E11

Kohara Phage

Genobase

PMID:3038334[7]

10B4

Kohara Phage

Genobase

PMID:3038334[7]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: % [8]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: 24% [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:EG11324

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11324

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001295

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947388

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1300

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009545

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. ↑ 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 Nakahigashi, K et al. (1992) Isolation and characterization of a light-sensitive mutant of Escherichia coli K-12 with a mutation in a gene that is required for the biosynthesis of ubiquinone. J. Bacteriol. 174 7352-9 PubMed
  5. ↑ 5.0 5.1 5.2 5.3 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
  6. ↑ 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
  7. ↑ 7.0 7.1 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
  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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