Difference between revisions of "Sandbox"

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* '''Description:''' RNA polymerase beta' subunit <br/><br/>
+
* '''Description:''' 23S rRNA<br/><br/>
  
 
{| align="right" border="1" cellpadding="2"  
 
{| align="right" border="1" cellpadding="2"  
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
 
|style="background:#ABCDEF;" align="center"|'''Gene name'''
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|''rpoC''
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|''rrnA-23S''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase beta' subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-23S
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || transcription
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 133 kDa, 8.863 
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|style="background:#ABCDEF;" align="center"| '''Gene length''' || 2928 bp
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3597 bp, 1199 aa
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnA-Ala]]'', ''[[rrnA-5S]]''
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpoB]]'', ''[[ybxF]]''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnA-23S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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|colspan="2" style="background:#FAF8CC;" align="center"|'''Get the DNA and protein [http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+&#91;EMBLCDS:CAB11884&#93;+-newId sequences] <br/> (Barbe ''et al.'', 2009)'''
+
|colspan="2" | '''Genetic context''' <br/> [[Image:rrnA-23S_context.gif]]
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|-
 
−
|-
 
−
|-
 
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|colspan="2" | '''Genetic context''' <br/> [[Image:rpoC_context.gif]]
 
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
  <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
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=== Basic information ===
 
=== Basic information ===
  
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* '''Locus tag:''' BSU01080
+
* '''Locus tag:'''
  
 
===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
essential [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
 
  
 
=== Database entries ===
 
=== Database entries ===
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* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG10729]
+
* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00014]
−
 
 
−
=== Additional information===
 
−
 
 
−
 
 
−
=The protein=
 
−
 
 
−
=== Basic information/ Evolution ===
 
−
 
 
−
* '''Catalyzed reaction/ biological activity:''' Nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1) (according to Swiss-Prot)
 
−
 
 
−
* '''Protein family:''' RNA polymerase beta' chain family (according to Swiss-Prot)
 
−
 
 
−
* '''Paralogous protein(s):'''
 
−
 
 
−
=== Extended information on the protein ===
 
−
 
 
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* '''Kinetic information:'''
 
−
 
 
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* '''Domains:'''
 
−
 
 
−
* '''Modification:'''
 
−
 
 
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* '''Cofactor(s):'''
 
−
 
 
−
* '''Effectors of protein activity:'''
 
−
 
 
−
* '''Interactions:''' [[RpoA]]-[[RpoB]]-[[RpoC]]
 
−
 
 
−
* '''Localization:''' membrane associated [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
 
−
 
 
−
=== Database entries ===
 
  
 
* '''Structure:'''
 
* '''Structure:'''
  
−
* '''Swiss prot entry:''' [http://www.uniprot.org/uniprot/P37871 P37871]
+
=== Additional information===
−
 
 
−
* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu+BSU01080]
 
−
 
 
−
* '''E.C. number:''' [http://www.expasy.org/enzyme/2.7.7.6 2.7.7.6]
 
  
−
=== Additional information===
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
+
* '''Operon:''' ''[[rrnA-16S]]-[[trnA-Ile]]-[[trnA-Ala]]-[[rrnA-23S]]-[[rrnA-5S]]'' [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
−
* '''[[Sigma factor]]:'''  
+
* '''Sigma factor:''' [[SigA]] [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:'''  
+
* '''Additional information:'''
  
 
=Biological materials =
 
=Biological materials =
Line 109: Line 67:
 
          
 
          
 
* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
−
 
−
* '''GFP fusion:'''
 
  
 
* '''two-hybrid system:'''  
 
* '''two-hybrid system:'''  
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* '''Antibody:'''
 
* '''Antibody:'''
  
−
=Labs working on this gene/protein=
+
=Labs working on this gene/RNA=
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
−
<pubmed>18763711, </pubmed>
+
<pubmed>6312418, </pubmed>
−
# Hahne et al. (2008) From complementarity to comprehensiveness - targeting the membrane proteome of growing ''Bacillus subtilis'' by divergent approaches. Proteomics '''8:''' 4123-4136 [http://www.ncbi.nlm.nih.gov/pubmed/18763711 PubMed]
+
# Ogasawara et al. (1983) Structure and organization of rRNA operons in the region of the replication origin of the ''Bacillus subtilis'' chromosome.''Nucl. Acids Res.'' '''11:''' 6301-6318. [http://www.ncbi.nlm.nih.gov/sites/entrez/6312418 PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]

Revision as of 14:34, 8 June 2009

  • Description: 23S rRNA

Gene name rrnA-23S
Synonyms
Essential no
Product ribosomal RNA-23S
Function translation
Gene length 2928 bp
Immediate neighbours trnA-Ala, rrnA-5S
Gene sequence (+200bp)
Genetic context
RrnA-23S context.gif
This image was kindly provided by SubtiList





The gene

Basic information

  • Locus tag:

Phenotypes of a mutant

Database entries

  • DBTBS entry: no entry
  • SubtiList entry: [1]
  • Structure:

Additional information

Expression and regulation

  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:
  • two-hybrid system:
  • Antibody:

Labs working on this gene/RNA

Your additional remarks

References

  1. Ogasawara et al. (1983) Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome.Nucl. Acids Res. 11: 6301-6318. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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