ubiD: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|   id="B46aa00549ba42"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ubiD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ubiD''
Ubiquinone
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3835, b3843, JW3819, yigC, yigY''<ref name='LIB:Riley_2006'/>, yigY''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18245.B46aa00549ba42&page=18245&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3835, b3843, JW3819, yigC, yigY''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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<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="Z46aa00552a025"  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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86.71 minutes&nbsp;
86.71 minutes&nbsp;
|
|
MG1655: 4023011..4024504<br />{{GBrowseFigureByCoord|4022011|4025504|ecoli|MG1655}}
MG1655: 4023011..4024504<br /><gbrowseImage>
name=NC_000913:4023011..4024504
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11396 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11396 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4022011..4025504 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4022011|4025504|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4023011..4024504&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4023011|4024504|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4003459..4004952<br /><gbrowseImage>
name=NC_012967:4003459..4004952
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4003459|4004952|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4003459|4004952|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3912680..3914173<br /><gbrowseImage>
name=NC_012759:3912680..3914173
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3912680|3914173|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3912680|3914173|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3611693..3610200<br />{{GBrowseFigureByCoord|3609200|3612693|ecoli_W3110|W3110}}  
W3110: 3611693..3610200<br /><gbrowseImage>
name=NC_007779:3610200..3611693
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3609200|3612693|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3610200|3611693|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3609200..3612693 GBrowse(W3110)]
DH10B: 4121931..4123424<br /><gbrowseImage>
name=NC_010473:4121931..4123424
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3610200..3611693&plugin_action=Go FASTA Dump]
{{GBrowseLink|DH10B|NC_010473|4118945|4126410|GBrowse(DH10B)}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46aa0055e31ad"  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
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====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46aa00563940b"  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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
|
ubiDG452R
|
 
|
G452R
|
 
|
(in AN66; inactive protein)
|
 
|
 
|
Strain variation; seeded from [http://www.uniprot.org/uniprot/P0AAB4 UniProt:P0AAB4]
|-
|
''ubiD410''
|
|
&Delta;ubiD (Keio:)
 
|
|
deletion
 
|
|
deletion
 
|
|


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|
|
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[[cgscmutation:9931|CGSC:9931]]
|
|
   
   
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''ubiD''::Tn''10''dCam
|
 
|
 
|
Mutagenesis rate
|
Decreased stress-induced mutagenesis (SIM) phenotype.
|
PMID:23224554
|
Parental Strain: SMR4562
 
Experimental Strain: SMR12313
|
Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
|-
|
SMR4562 yiaG-yfp FRT ''ubiD''::Tn''10''dCam
|
insertion
|
 
|
Sigma<sup>S</sup> activity
|
Decrease in Sigma<sup>S</sup> activity
|
PMID:23224554
|
Parental Strain: SMR10582
Experimental Strain: SMR13098
|
See table S8 for full experimental data.
|-
|
CAG45114 ''ubiD''::Tn''10''dCam
|
insertion
|
 
|
Sigma<sup>E</sup> activity
|
Decrease in Sigma<sup>E</sup> activity
|
PMID:23224554
 
|
Parental Strain: CAG45114
Experimental Strain: SMR15323
|
See table S11 for full experimental data.
 
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===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW3819
JW3819
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGGCGCTTTTACCGTTGTTAAA  
Primer 2:CCGGCGCTTTTACCGTTGTTAAA  
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[[:Category:Kohara_Phage:16G1|16G1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=550 Genobase]
|
PMID:3038334
|-
|
metEo-3079::Tn10
|
Linked marker
|
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 60% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
|-
|
[[fadA:Gene|fad-751::Tn10]]
|
Linked marker
|
CAG18496 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40344 CGSC7465]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:fadAB101::Tn10
 
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11396 EcoCyc:EG11396] 
EcoCyc:EG11396
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|
''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=EB1369 EchoBASE:EB1369] 
EcoGene:EG11396
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|
''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=b3843 EcoliGenExpDB:b3843] 
RegulonDB:ECK120001363
|
|
''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=C4790 ECOL199310CYC:C4790]
[http://www.ncbi.nlm.nih.gov/gene?term=948326 GeneID:948326]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11396 EcoGene:EG11396] 
EchoBASE:EB1369
|
|
''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=YIGC ECOO157CYC:YIGC] 
ASAP:ABE-0012557
|
|
''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 not 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 20:50, 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

ubiD

Mnemonic

Ubiquinone

Synonyms

ECK3835, b3843, JW3819, yigC, yigY[1], yigY

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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

86.71 minutes 

MG1655: 4023011..4024504
<gbrowseImage> name=NC_000913:4023011..4024504 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4003459..4004952
<gbrowseImage> name=NC_012967:4003459..4004952 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3912680..3914173
<gbrowseImage> name=NC_012759:3912680..3914173 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3611693..3610200
<gbrowseImage> name=NC_007779:3610200..3611693 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4121931..4123424
<gbrowseImage> name=NC_010473:4121931..4123424 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

ubiDG452R

G452R

(in AN66; inactive protein)

Strain variation; seeded from UniProt:P0AAB4

ubiD410

CGSC:9931

ubiD::Tn10dCam

Mutagenesis rate

Decreased stress-induced mutagenesis (SIM) phenotype.

PMID:23224554[2]

Parental Strain: SMR4562

Experimental Strain: SMR12313

Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.

SMR4562 yiaG-yfp FRT ubiD::Tn10dCam

insertion

SigmaS activity

Decrease in SigmaS activity

PMID:23224554[2]

Parental Strain: SMR10582 Experimental Strain: SMR13098

See table S8 for full experimental data.

CAG45114 ubiD::Tn10dCam

insertion

SigmaE activity

Decrease in SigmaE activity

PMID:23224554[2]

Parental Strain: CAG45114 Experimental Strain: SMR15323

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

JW3819

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCGACGCCATGAAATATAACGA

Primer 2:CCGGCGCTTTTACCGTTGTTAAA

16G1

Kohara Phage

Genobase

PMID:3038334[4]

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[5]

est. P1 cotransduction: 60% [6]
Synonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[5]

est. P1 cotransduction: 87% [6]
Synonyms:fadAB101::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:EG11396

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11396

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001363

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948326

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1369

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012557

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 2.2 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
  3. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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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