epd: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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''epd''  
''epd''  
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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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''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2923, b2927, JW2894, gapB, gap2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
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****************************************************************************************** -->{{Gene_location_help}}
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{|  id="G46a9e994bf3fb"  class=" tableEdit Gene_location_table"   
{|  id="G46a9e994bf3fb"  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: 2958423..2959442<br />{{GBrowseFigureByCoord|2958423|2959442|REL606|NC_012967}}
NC_012967: 2959442..2958423<br />{{GBrowseFigureByCoord|2958423|2959442|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|2958423|2959442|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|2958423|2959442|GBrowse (REL606)}}
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|  id="B46a9e9957c6ca"  class=" tableEdit Gene_sequence_features_table"   
{|  id="B46a9e9957c6ca"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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{|   id="A46a9e995c3bd6"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="A46a9e995c3bd6"  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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{|  id="N46a9e99680248"  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="L46a9e997251db"  class=" tableEdit Gene_accessions_table"   
{|  id="L46a9e997251db"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:20, 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

epd

Mnemonic
Synonyms

ECK2923, b2927, JW2894, gapB, gap2[1][2]

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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

66.18 minutes 

MG1655: 3071713..3070694
gbrowse_img.php?coord=3070694..3071713&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2959442..2958423
gbrowse_img.php?coord=2958423..2959442&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 3072347..3071328
gbrowse_img.php?coord=3071328..3072347&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3165583..3164564
gbrowse_img.php?coord=3164564..3165583&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

Δepd (Keio:JW2894)

deletion

deletion

PMID:16738554[3]

Shigen

epd::Tn5KAN

PMID:12519969[4]

ASAP

At position 643 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20979

epd::Tn5KAN

PMID:12519969[4]

ASAP

At position 643 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20980

Δepd-11::Ery

PMID:9260967[5]

CGSC:60142


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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

JW2894

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCACCGTACGCGTAGCGATAAA

Primer 2:CCtCTGAAAGCAACAGTAGCCAT

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[7]

est. P1 cotransduction: % [8]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[7]

est. P1 cotransduction: 60% [8]
Synonyms:zgd-210::Tn10, zgf-210::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:EG10368

EchoBASE (EcoliWiki Page)

EchoBASE:EB0363

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2927

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3505

EcoGene (EcoliWiki Page)

EcoGene:EG10368

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:EPD

CGSC (EcoliWiki Page)

CGSC:32089

ASAP (EcoliWikiPage)

ASAP:ABE-0009607


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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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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 Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  5. ↑ Seta, FD et al. (1997) Characterization of Escherichia coli strains with gapA and gapB genes deleted. J. Bacteriol. 179 5218-21 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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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