yaaI:Gene: Difference between revisions

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Update TableEdit tables.
Fixing REL gene coord display.
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!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
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''yaaI''  
''yaaI''  
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!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0013, b0013, JW0012''<ref name='LIB:Riley_2006'/>
''ECK0013, b0013, JW0012''<ref name='LIB:Riley_2006'/>
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{|  id="S46a9a66bc0d21"  class=" tableEdit Gene_location_table"   
{|  id="S46a9a66bc0d21"  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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NC_012967: 11380..11784<br />{{GBrowseFigureByCoord|11380|11784|REL606|NC_012967}}
NC_012967: 11784..11380<br />{{GBrowseFigureByCoord|11380|11784|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|11380|11784|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|11380|11784|GBrowse (REL606)}}
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{|  id="Y46a9a66c68378"  class=" tableEdit Gene_sequence_features_table"   
{|  id="Y46a9a66c68378"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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{| {{Prettytable}}  id="C46a9a66ca820c"  class=" tableEdit Gene_allele_table"   
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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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!|Resource!!Resource Type!!Source!!Notes/Reference
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!|Database!!Accession!!Notes
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!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:56, 21 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

yaaI

Mnemonic
Synonyms

ECK0013, b0013, JW0012[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

0.25 minutes 

MG1655: 11786..11382
gbrowse_img.php?coord=11382..11786&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 11784..11380
gbrowse_img.php?coord=11380..11784&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 11786..11382
gbrowse_img.php?coord=11382..11786&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 11786..11382
gbrowse_img.php?coord=11382..11786&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

yaaI::Tn5KAN

PMID:12519969[2]

ASAP

At position 299 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20004

ΔyaaI (Keio:JW0012)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8341[4]

yaaI::Tn5KAN

PMID:12519969[2]

ASAP

At position 299 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20003

ΔyaaI733::kan

PMID:16738554[3]

CGSC:103440


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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

JW0012

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAATCCGTTTTTACGATTTC

Primer 2:CCGTCGTCGCCGATAATTTTCAG

thrA34::Tn10

Linked marker

CAG18442 = CGSC7320[4]

est. P1 cotransduction: 68% [6]
Synonyms:thr-34::Tn10

carB96::Tn10

Linked marker

CAG12093 = CGSC7322[4]

est. P1 cotransduction: 46% [6]
Synonyms:car-96::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:G8202

EchoBASE (EcoliWiki Page)

EchoBASE:EB1475

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0013

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0017

EcoGene (EcoliWiki Page)

EcoGene:EG11513

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAAI

ASAP (EcoliWikiPage)

ASAP:ABE-0000043


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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. ↑ 2.0 2.1 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  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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