ubiD:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3835, b3843, JW3819, yigC, yigY''<ref name='LIB:Riley_2006'/>
''ECK3835, b3843, JW3819, yigC, yigY''<ref name='LIB:Riley_2006'/>, yigY''


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{|   id="Z46aa00552a025"  class=" tableEdit Gene_location_table"   
{| 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"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[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]
{{GBrowseLink|ecoli|NC_000913|4022011|4025504|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|4022011|4025504|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|4023011|4024504|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]  
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{{GBrowseLink|BW2952|012759|3912680|NC_3914173|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3912680|3914173|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|3912680|NC_3914173|FASTA Dump}}  
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W3110: 3611693..3610200<br /><gbrowseImage>
W3110: 3611693..3610200<br /><gbrowseImage>
name=AC_000091:3610200..3611693
name=NC_007779:3610200..3611693
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3609200|3612693|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3609200|3612693|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3610200|3611693|FASTA Dump}}  
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DH10B: 4121931..4123424<br /><gbrowseImage>
DH10B: 4121931..4123424<br /><gbrowseImage>
name=NC_010473:4121931..4123424
name=NC_010473:4121931..4123424
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|4118945|4126410|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|4118945|4126410|GBrowse(DH10B)}}
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{|   id="Y46aa0055e31ad"  class=" tableEdit Gene_sequence_features_table"   
{| 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"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{| {{Prettytable}} id="S46aa00563940b"  class=" tableEdit Gene_allele_table dataTable"   
{| 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"   
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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''ubiD''::Tn''10''dCam
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Mutagenesis rate
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Decreased stress-induced mutagenesis (SIM) phenotype.
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PMID:23224554
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Parental Strain: SMR4562
Experimental Strain: SMR12313
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Mutation Rate was comparatively weak, to other strains, with decrease only happening in 33-67% of wild type population.
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SMR4562 yiaG-yfp FRT ''ubiD''::Tn''10''dCam
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insertion
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Sigma<sup>S</sup> activity
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Decrease in Sigma<sup>S</sup> activity
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PMID:23224554
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Parental Strain: SMR10582
Experimental Strain: SMR13098
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See table S8 for full experimental data.
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CAG45114 ''ubiD''::Tn''10''dCam
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insertion
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Sigma<sup>E</sup> activity
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Decrease in Sigma<sup>E</sup> activity
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PMID:23224554
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Parental Strain: CAG45114
Experimental Strain: SMR15323
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See table S11 for full experimental data.


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{|   id="P4e04c5243f4bf"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="P4e04c5243f4bf"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="L46aa0056f29ed"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aa0056f29ed"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGGCGCTTTTACCGTTGTTAAA  
Primer 2:CCGGCGCTTTTACCGTTGTTAAA  
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[[:Category:Kohara_Phage:16G1|16G1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=550 Genobase]
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PMID:3038334
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{|   id="L46aa00579e477"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46aa00579e477"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11396 EcoCyc:EG11396]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1369 EchoBASE:EB1369]
EcoCyc:EG11396
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3843 EcoliGenExpDB:b3843]
EcoGene:EG11396
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
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[http://BioCyc.org/ECOL199310/new-image?object=C4790 ECOL199310CYC:C4790]
RegulonDB:ECK120001363
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11396 EcoGene:EG11396]
[http://www.ncbi.nlm.nih.gov/gene?term=948326 GeneID:948326]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YIGC ECOO157CYC:YIGC]
EchoBASE:EB1369
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012557&formSubmitReturn=1 ASAP:ABE-0012557]
ASAP:ABE-0012557
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:50, 19 September 2013

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

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

edit table


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.

edit table


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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<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 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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