trg:Gene: Difference between revisions

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Revision as of 22:10, 26 July 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 Sequence Features 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

trg

Mnemonic

Taxis to ribose and galactose

Synonyms

ECK1415, b1421, JW1417[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

32.12 minutes 

MG1655: 1490494..1492134
<gbrowseImage> name=NC_000913:1490494..1492134 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1462579..1464219
<gbrowseImage> name=NC_012967:1462579..1464219 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1382553..1384193
<gbrowseImage> name=NC_012759:1382553..1384193 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1494184..1495824
<gbrowseImage> name=AC_000091:1494184..1495824 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1581089..1582729
<gbrowseImage> name=NC_010473:1581089..1582729 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

Δtrg (Keio:JW1417)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9242[3]

trg

PMID:12519969[4]

ASAP

At position 509 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20316

trg

PMID:12519969[4]

ASAP

At position 509 in Minus orientation, does not contain plasmid pKD46.
ASAP strain name: FB20317

trg-2::Tn10

Insertion at 1,491,930 bp in MG1655 (NC_000913)

adapted from Nichols et al.[5]

CAG12026 = CGSC7376[3]

Synonyms:

trg-1::Tn5

CGSC:9685

trg-2::Tn10

PMID:2540407[6]

CGSC:10754

trg-3120::Tn10kan

PMID:2540407[6]

CGSC:39820

Δtrg-782::kan

PMID:16738554[2]

CGSC:103208


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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

JW1417

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAATACAACTCCCTCACAGCG

Primer 2:CCaACCGTAGCGAAACTAACTGG

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 6% [5]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: 13% [5]
Synonyms:zdc-235::Tn10

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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:EG11018

EchoBASE (EcoliWiki Page)

EchoBASE:EB1011

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1421

EcoGene (EcoliWiki Page)

EcoGene:EG11018

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:TRG

CGSC (EcoliWiki Page)

CGSC:85

ASAP (EcoliWikiPage)

ASAP:ABE-0004744


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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 3.3 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. ↑ 5.0 5.1 5.2 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).
  6. ↑ 6.0 6.1 Singer, M et al. (1989) A collection of strains containing genetically linked alternating antibiotic resistance elements for genetic mapping of Escherichia coli. Microbiol. Rev. 53 1-24 PubMed
  7. ↑ 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

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