rhaS:Gene: Difference between revisions

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Refreshing information from GenBank record NC_000913
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10843 ECOCYC:EG10843]
EcoCyc:EG10843
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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[http://ecogene.org/geneinfo.php?eg_id=EG10843 EcoGene:EG10843]
EcoGene:EG10843
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Escherichia coli str. K-12 substr. MG1655  
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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Escherichia coli str. K-12 substr. MG1655  
Escherichia coli str. K-12 substr. MG1655  
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[[RegulonDB]]
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RegulonDB:ECK120000834
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB0836
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[ASAP]]
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ASAP:ABE-0012745
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:33, 27 May 2013

{{#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 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], rhaC2

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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=MG1655 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=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4195456..4196292
<gbrowseImage> name=NC_010473:4195456..4196292 source=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

4B6

Kohara Phage

Genobase

PMID:3038334[4]

7G8

Kohara Phage

Genobase

PMID:3038334[4]

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[5]

est. P1 cotransduction: 29% [6]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[5]

est. P1 cotransduction: 12% [6]
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

EcoCyc:EG10843

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10843

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948397

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000834

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0836

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012745

Escherichia coli str. K-12 substr. MG1655

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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. ↑ 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 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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