yadI: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=EG12322 EcoCyc:EG12322]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12322 EcoCyc:EG12322]
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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=EB2227 EchoBASE:EB2227]
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2227 EchoBASE:EB2227]
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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=b0129 EcoliGenExpDB:b0129]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0129 EcoliGenExpDB:b0129]
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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=C0158 ECOL199310CYC:C0158]
[http://BioCyc.org/ECOL199310/new-image?object=C0158 ECOL199310CYC:C0158]
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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=EG12322 EcoGene:EG12322]
[http://ecogene.org/geneinfo.php?eg_id=EG12322 EcoGene:EG12322]
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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=YADI ECOO157CYC:YADI]
[http://BioCyc.org/ECOO157/new-image?object=YADI ECOO157CYC:YADI]
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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=0000453&formSubmitReturn=1 ASAP:ABE-0000453] 
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Revision as of 22:22, 15 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

yadI

Mnemonic
Synonyms

ECK0128, b0129, JW0125, agaX[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

3.12 minutes 

MG1655: 144577..145017
gbrowse_img.php?coord=143577..146017&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 144577..145017
gbrowse_img.php?coord=143577..146017&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

ΔyadI (Keio:JW0125)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8402[3]

ΔyadI746::kan

PMID:16738554[2]

CGSC:103468


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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

JW0125

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTTAGGTTGGGTAATTACCTG

Primer 2:CCATACTCATACAAATTATGTTT

leuO3051::Tn10

Linked marker

CAG12095 = CGSC7324[3]

est. P1 cotransduction: 4% [5]

Synonyms:zab-3051::Tn10


The start of leuO was reannotated by Riley et al. (2006).

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 88% [5]

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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:EG12322

EchoBASE (EcoliWiki Page)

EchoBASE:EB2227

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0129

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0158

EcoGene (EcoliWiki Page)

EcoGene:EG12322

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YADI

ASAP (EcoliWikiPage)

ASAP:ABE-0000453


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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. ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 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
  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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