aspA: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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''aspA''  
''aspA''  
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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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''ECK4133, b4139, JW4099''<ref name='LIB:Riley_2006'/>
''ECK4133, b4139, JW4099''<ref name='LIB:Riley_2006'/>
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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NC_012967: 4345612..4347048<br />{{GBrowseFigureByCoord|4345612|4347048|REL606|NC_012967}}
NC_012967: 4347048..4345612<br />{{GBrowseFigureByCoord|4345612|4347048|REL606|NC_012967}}
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{{GBrowseLink|REL606|NC_012967|4345612|4347048|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|4345612|4347048|GBrowse (REL606)}}
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!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


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!|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
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Revision as of 20:11, 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

aspA

Mnemonic
Synonyms

ECK4133, b4139, JW4099[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

94.08 minutes, 94.08 minutes 

MG1655: 4366350..4364914
gbrowse_img.php?coord=4364914..4366350&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4347048..4345612
gbrowse_img.php?coord=4345612..4347048&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4373007..4371571
gbrowse_img.php?coord=4371571..4373007&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4466712..4465276
gbrowse_img.php?coord=4465276..4466712&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

ΔaspA (Keio:JW4099)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8324[3]

aspA22

CGSC:5112

aspA23

CGSC:5113

ΔaspA765::kan

PMID:16738554[2]

CGSC:100110


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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

JW4099

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCAAACAACATTCGTATCGA

Primer 2:CCtTGTTCGCTTTCATCAGTATA

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[3]

est. P1 cotransduction: 76% [5]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[3]

est. P1 cotransduction: 4% [5]

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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:EG10095

EchoBASE (EcoliWiki Page)

EchoBASE:EB0093

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4139

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5222

EcoGene (EcoliWiki Page)

EcoGene:EG10095

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ASPA

CGSC (EcoliWiki Page)

CGSC:991

ASAP (EcoliWikiPage)

ASAP:ABE-0013551


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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. ↑ 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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