ubiD:Gene: Difference between revisions

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!Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11396 EcoCyc:EG11396]
[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]])  
[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]
[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]])  
[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]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3843 EcoliGenExpDB:b3843]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
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[http://BioCyc.org/ECOL199310/new-image?object=C4790 ECOL199310CYC:C4790]
[http://BioCyc.org/ECOL199310/new-image?object=C4790 ECOL199310CYC:C4790]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
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[http://ecogene.org/geneinfo.php?eg_id=EG11396 EcoGene:EG11396]
[http://ecogene.org/geneinfo.php?eg_id=EG11396 EcoGene:EG11396]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
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[http://BioCyc.org/ECOO157/new-image?object=YIGC ECOO157CYC:YIGC]
[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 00:55, 16 September 2008

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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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Standard name

ubiD

Mnemonic
Synonyms

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

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

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Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

86.71 minutes 

MG1655: 4023011..4024504
gbrowse_img.php?coord=4022011..4025504&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3611693..3610200
gbrowse_img.php?coord=3609200..3612693&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

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See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

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Feature type Location Description
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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ubiD410

CGSC:9931


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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

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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


The 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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See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

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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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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Notes

Links

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Name URL Comments
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See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

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).


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