alkB: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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''alkB''  
''alkB''  
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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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''ECK2204, b2212, JW2200, aidD''<ref name='LIB:Riley_2006'/>
''ECK2204, b2212, JW2200, aidD''<ref name='LIB:Riley_2006'/>
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{|  id="L46a9d8a764cee"  class=" tableEdit Gene_location_table"   
{|  id="L46a9d8a764cee"  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: 2258795..2259445<br />{{GBrowseFigureByCoord|2258795|2259445|REL606|NC_012967}}
NC_012967: 2259445..2258795<br />{{GBrowseFigureByCoord|2258795|2259445|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|2258795|2259445|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|2258795|2259445|GBrowse (REL606)}}
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{|  id="L46a9d8a81b025"  class=" tableEdit Gene_sequence_features_table"   
{|  id="L46a9d8a81b025"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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{|   id="Y46a9d8a85ff11"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="Y46a9d8a85ff11"  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 20:07, 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

alkB

Mnemonic
Synonyms

ECK2204, b2212, JW2200, aidD[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

49.72 minutes, 49.72 minutes 

MG1655: 2307363..2306713
gbrowse_img.php?coord=2306713..2307363&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 2259445..2258795
gbrowse_img.php?coord=2258795..2259445&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 2312675..2312025
gbrowse_img.php?coord=2312025..2312675&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 2398351..2397701
gbrowse_img.php?coord=2397701..2398351&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

ΔalkB (Keio:JW2200)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9779[3]

alkB

PMID:12519969[4]

ASAP

At position 334 in Plus orientation, contains plasmid pKD46.
ASAP strain name: FB20706

alkB

PMID:12519969[4]

ASAP

At position 334 in Plus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20707

ΔalkB765::kan

PMID:16738554[2]

CGSC:99968


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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

JW2200

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTGGATCTGTTTGCCGATGC

Primer 2:CCTTCTTTTTTACCTGCCTGACG

napA722::Tn10

Linked marker

CAG12098 = CGSC7400[3]

est. P1 cotransduction: 83% [6]
Synonyms:zeg-722, zei-722::Tn10

atoS298::Tn10

Linked marker

CAG12177 gyrA+ = CGSC7525[3]

est. P1 cotransduction: 63% [6]
Synonyms:zeh-298::Tn10, zej-298::Tn10 nnnThe original CAG12177 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

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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:EG10037

EchoBASE (EcoliWiki Page)

EchoBASE:EB0036

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2212

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2753

EcoGene (EcoliWiki Page)

EcoGene:EG10037

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ALKB

CGSC (EcoliWiki Page)

CGSC:18544

ASAP (EcoliWikiPage)

ASAP:ABE-0007308


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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 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. ↑ 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. ↑ 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).

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