ubiD:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Standard name
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''ubiD''  
''ubiD''  
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!align=left {{table_heading_style}} |Mnemonic
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!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'/>


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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11396 EcoCyc Sequence Dump]  
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[[REL606]]
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NC_012967: 4003459..4004952<br />{{GBrowseFigureByCoord|4003459|4004952|REL606|NC_012967}}
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NC_012967: 4003459..4004952<br />{{GBrowseFigureByCoord|4003459|4004952|REL606|NC_012967}}
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!|Feature type!!Location!!Description
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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Synonyms:fadAB101::Tn10  
Synonyms:fadAB101::Tn10  


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Revision as of 01:05, 10 January 2010

{{#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 Alleles and Phenotypes 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
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
gbrowse_img.php?coord=4023011..4024504&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4003459..4004952
gbrowse_img.php?coord=4003459..4004952&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3611693..3610200
gbrowse_img.php?coord=3610200..3611693&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4121931..4123424
gbrowse_img.php?coord=4121931..4123424&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

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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 Location Description
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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

ubiD410

CGSC:9931


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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

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[3]

est. P1 cotransduction: 60% [4]
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[3]

est. P1 cotransduction: 87% [4]
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 (EcoliWiki Page)

EcoCyc:EG11396

EchoBASE (EcoliWiki Page)

EchoBASE:EB1369

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3843

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4790

EcoGene (EcoliWiki Page)

EcoGene:EG11396

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YIGC

ASAP (EcoliWikiPage)

ASAP:ABE-0012557


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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. ↑ 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. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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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