rhaS:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:59, 24 June 2011

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features Alleles and Phenotypes Genetic Interactions 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

rhaS

Mnemonic

Rhamnose

Synonyms

ECK3898, b3905, JW3876, rhaC, rhaC2[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

88.28 minutes 

MG1655: 4095759..4096595
<gbrowseImage> name=NC_000913:4095759..4096595 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4077218..4078054
<gbrowseImage> name=NC_012967:4077218..4078054 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3985428..3986264
<gbrowseImage> name=NC_012759:3985428..3986264 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3538945..3538109
<gbrowseImage> name=AC_000091:3538109..3538945 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4195456..4196292
<gbrowseImage> name=NC_010473:4195456..4196292 source=ecoli_DH10B preset=GeneLocation </gbrowseImage>

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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

ΔrhaS (Keio:JW3876)

deletion

deletion

PMID:16738554[2]

Shigen

rhaSR202A

R202A

4% of wild-type activity

seeded from UniProt:P09377

rhaSS255A

S255A

80% of wild-type activity

seeded from UniProt:P09377

rhaST256A

T256A

61% of wild-type activity

seeded from UniProt:P09377

rhaSS249G

S249G

93% of wild-type activity

seeded from UniProt:P09377

rhaSD250A

D250A

8.3% of wild-type activity

seeded from UniProt:P09377

rhaSS251G

S251G

87% of wild-type activity

seeded from UniProt:P09377

rhaSF248V

F248V

3.3% of wild-type activity

seeded from UniProt:P09377

rhaSF254A

F254A

1.2% of wild-type activity

seeded from UniProt:P09377

rhaSL201A

L201A

48% of wild-type activity

seeded from UniProt:P09377

rhaSF248A

F248A

0.9% of wild-type activity

seeded from UniProt:P09377

rhaSN252H

N252H

0.4% of wild-type activity

seeded from UniProt:P09377

rhaSN252I

N252I

0.3% of wild-type activity

seeded from UniProt:P09377

rhaSN252S

N252S

37% of wild-type activity

seeded from UniProt:P09377

rhaSH253A

H253A

48% of wild-type activity

seeded from UniProt:P09377

rhaSH253Q

H253Q

32% of wild-type activity

seeded from UniProt:P09377

rhaSN252A

N252A

31% of wild-type activity

seeded from UniProt:P09377

rhaSH205A

H205A

28% of wild-type activity

seeded from UniProt:P09377

rhaSR206A

R206A

0.1% of wild-type activity

seeded from UniProt:P09377

rhaSC246A

C246A

66% of wild-type activity

seeded from UniProt:P09377

rhaSG247A

G247A

6.2% of wild-type activity

seeded from UniProt:P09377

rhaSG247R

G247R

0.9% of wild-type activity

seeded from UniProt:P09377

xx

xx

xx

Growth Phenotype

xx


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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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

JW3876

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCACCGTATTACATAGTGTGGA

Primer 2:CCTTGCAGAAAGCCATCCCGTCC

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[4]

est. P1 cotransduction: 29% [5]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[4]

est. P1 cotransduction: 12% [5]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (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:EG10843

EchoBASE (EcoliWiki Page)

EchoBASE:EB0836

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3905

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4855

EcoGene (EcoliWiki Page)

EcoGene:EG10843

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:RHAS

CGSC (EcoliWiki Page)

CGSC:17950

ASAP (EcoliWikiPage)

ASAP:ABE-0012745


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Notes

Links

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<protect>

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. ↑ 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. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  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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