ubiD:Gene: Difference between revisions

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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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est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/> <br />  
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/> <br />  
Synonyms:fadAB101::Tn10  
Synonyms:fadAB101::Tn10  
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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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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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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]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3843 EcoliGenExpDB:b3843]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C4790 ECOL199310CYC:C4790]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11396 EcoGene:EG11396]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=YIGC ECOO157CYC:YIGC]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012557&formSubmitReturn=1 ASAP:ABE-0012557]
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Revision as of 21:44, 21 September 2011

{{#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]

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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=AC_000091:3610200..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


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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[2]

Status:Clone OK

Primer 1:GCCGACGCCATGAAATATAACGA

Primer 2:CCGGCGCTTTTACCGTTGTTAAA

16G1

Kohara Phage

Genobase

PMID:3038334[3]

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[4]

est. P1 cotransduction: 60% [5]
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[4]

est. P1 cotransduction: 87% [5]
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
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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. ↑ 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
  3. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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