psd:Gene: Difference between revisions

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!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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Revision as of 23:19, 10 May 2010

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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

psd

Mnemonic

Phosphatidylserine decarboxylase

Synonyms

ECK4156, b4160, JW4121[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

94.56 minutes 

MG1655: 4388383..4387415
gbrowse_img.php?coord=4387415..4388383&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4368515..4367547
gbrowse_img.php?coord=4367547..4368515&genome=REL606&name=NC_012967&trackset=0&width=300&.png

BW2952

NC_012759: 4326150..4327118
gbrowse_img.php?coord=4326150..4327118&genome=BW2952&name=NC_012759&trackset=0&width=300&.png

W3110

 

W3110: 4395040..4394072
gbrowse_img.php?coord=4394072..4395040&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4488745..4487777
gbrowse_img.php?coord=4487777..4488745&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 Strain Genomic Location Evidence Reference Notes
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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

psdS254A

S254A

No processing of the proenzyme, complete loss of activity

seeded from UniProt:P0A8K1

psdS254C

S254C

Reduced processing, 16% wild-type activity

seeded from UniProt:P0A8K1

psdS254T

S254T

Reduced processing, 2% wild-type activity

seeded from UniProt:P0A8K1

psd-2(ts)

temperature sensitive

CGSC:8626


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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

JW4121

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCTTAAATTCATTTAAACTTTC

Primer 2:CCGACCTGGTCTTTTTTGTCGTC

cadB2231::Tn10

Linked marker

CAG18488 = CGSC7479[3]

est. P1 cotransduction: 30% [4]
Synonyms:zjd-2231::Tn10

cycA30::Tn10

Linked marker

CAG12073 = CGSC7482[3]

est. P1 cotransduction: 20% [4]

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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:EG10775

EchoBASE (EcoliWiki Page)

EchoBASE:EB0768

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4160

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5247

EcoGene (EcoliWiki Page)

EcoGene:EG10775

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z5766

CGSC (EcoliWiki Page)

CGSC:356

ASAP (EcoliWikiPage)

ASAP:ABE-0013623


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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).

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