tdcF: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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''tdcF''  
''tdcF''  
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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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''ECK3102, b3113, JW5521, yhaR''<ref name='LIB:Riley_2006'/>
''ECK3102, b3113, JW5521, yhaR''<ref name='LIB:Riley_2006'/>
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|  id="M46a9ede51d562"  class=" tableEdit Gene_location_table"   
{|  id="M46a9ede51d562"  class=" tableEdit Gene_location_table"   
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|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 3192755..3193144<br />{{GBrowseFigureByCoord|3192755|3193144|REL606|NC_012967}}
NC_012967: 3193144..3192755<br />{{GBrowseFigureByCoord|3192755|3193144|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|3192755|3193144|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3192755|3193144|GBrowse (REL606)}}
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|  id="J46a9ede5cfe5f"  class=" tableEdit Gene_sequence_features_table"   
{|  id="J46a9ede5cfe5f"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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{|   id="D46a9ede6237ee"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="D46a9ede6237ee"  class=" tableEdit Gene_allele_table"   
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|- {{table_heading_style}}
!|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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****************************************************************************************** -->{{Gene_resources_help}}
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{|  id="F46a9ede6d62a8"  class=" tableEdit Gene_resource_table"   
{|  id="F46a9ede6d62a8"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|  id="N46a9ede77d5ed"  class=" tableEdit Gene_accessions_table"   
{|  id="N46a9ede77d5ed"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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{|  id="T46a7098ead1af"  class=" tableEdit Links_table"   
{|  id="T46a7098ead1af"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:52, 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

tdcF

Mnemonic
Synonyms

ECK3102, b3113, JW5521, yhaR[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

70.21 minutes 

MG1655: 3258132..3257743
gbrowse_img.php?coord=3257743..3258132&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3193144..3192755
gbrowse_img.php?coord=3192755..3193144&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3258766..3258377
gbrowse_img.php?coord=3258377..3258766&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3355877..3355488
gbrowse_img.php?coord=3355488..3355877&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
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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

Plasmid clone

Shigen

PMID:16769691[2]

Status:

Primer 1:

Primer 2:

aer-3075::Tn10

Linked marker

CAG12152 = CGSC7438[3]

est. P1 cotransduction: 16% [4]
Synonyms:zgh-3075::Tn10, zgj-3075::Tn10

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[3]

est. P1 cotransduction: 1% [4]
Synonyms:zgj-203::Tn10, zha-203::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:G7626

EchoBASE (EcoliWiki Page)

EchoBASE:EB2611

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3113

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3871

EcoGene (EcoliWiki Page)

EcoGene:EG12757

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHAR

ASAP (EcoliWikiPage)

ASAP:ABE-0010240


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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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