hcaR: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=G7331 ECOCYC:G7331]
EcoCyc:G7331
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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=EG13455 EcoGene:EG13455]
EcoGene:EG13455
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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:ECK120003903
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[[EchoBASE]]
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EchoBASE:EB3228
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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-0008351
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Revision as of 07:25, 27 May 2013

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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

hcaR

Mnemonic

Hydrocinnamic acid

Synonyms

ECK2534, b2537, JW2521, yfhT, phdR[1], phdR

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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

57.46 minutes, 57.46 minutes 

MG1655: 2666918..2666028
<gbrowseImage> name=NC_000913:2666028..2666918 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2589595..2588705
<gbrowseImage> name=NC_012967:2588705..2589595 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2551833..2552723
<gbrowseImage> name=NC_012759:2551833..2552723 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2667552..2666662
<gbrowseImage> name=AC_000091:2666662..2667552 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2758683..2757793
<gbrowseImage> name=NC_010473:2757793..2758683 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

ΔhcaR (Keio:JW2521)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10007[3]

ΔhcaR782::kan

PMID:16738554[2]

CGSC:101316


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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

JW2521

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGAACTACGGCATTTACGCTA

Primer 2:CCTGCCGTTACGCTTGCCAAACG

5E10

Kohara Phage

Genobase

PMID:3038334[5]

6F10

Kohara Phage

Genobase

PMID:3038334[5]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[3]

est. P1 cotransduction: 91% [6]
Synonyms:zff-208::Tn10

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[3]

est. P1 cotransduction: 15% [6]

hcaR::cat

Strain

FB85

PMID:15808934[7]

hcaR::lacZ

Strain

FB82

PMID:15808934[7]

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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:G7331

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13455

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947000

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003903

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3228

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008351

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. ↑ 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 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
  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).
  7. ↑ 7.0 7.1 Turlin, E et al. (2005) 3-phenylpropionate catabolism and the Escherichia coli oxidative stress response. Res. Microbiol. 156 312-21 PubMed

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