Difference between revisions of "Sandbox"

From SubtiWiki
Jump to: navigation, search
Line 1: Line 1:
−
* '''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'''
−
|''rpoC''
+
|''rrnA-23S''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Essential''' || yes [http://www.ncbi.nlm.nih.gov/pubmed/12682299 PubMed]
+
|style="background:#ABCDEF;" align="center"| '''Essential''' || no
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Product''' || RNA polymerase beta' subunit
+
|style="background:#ABCDEF;" align="center"| '''Product''' || ribosomal RNA-23S
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Function''' || transcription
+
|style="background:#ABCDEF;" align="center"|'''Function''' || translation
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 133 kDa, 8.863 
+
|style="background:#ABCDEF;" align="center"| '''Gene length''' || 2928 bp
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 3597 bp, 1199 aa
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[trnA-Ala]]'', ''[[rrnA-5S]]''
 
|-
 
|-
−
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[rpoB]]'', ''[[ybxF]]''
+
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/rrnA-23S_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
−
|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]]
−
|-
 
−
|-
 
−
|-
 
−
|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>
 
|-
 
|-
Line 37: Line 33:
 
=== Basic information ===
 
=== Basic information ===
  
−
* '''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 ===
Line 47: Line 41:
 
* '''DBTBS entry:''' no entry
 
* '''DBTBS entry:''' no entry
  
−
* '''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 ===
 
−
 
 
−
* '''Kinetic information:'''
 
−
 
 
−
* '''Domains:'''
 
−
 
 
−
* '''Modification:'''
 
−
 
 
−
* '''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=
  
−
* '''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:'''  
Line 100: Line 58:
 
* '''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:'''  
Line 116: Line 72:
 
* '''Antibody:'''
 
* '''Antibody:'''
  
−
=Labs working on this gene/protein=
+
=Labs working on this gene/RNA=
  
 
=Your additional remarks=
 
=Your additional remarks=
Line 122: Line 78:
 
=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 13:34, 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

N Ogasawara, S Moriya, H Yoshikawa
Structure and organization of rRNA operons in the region of the replication origin of the Bacillus subtilis chromosome.
Nucleic Acids Res: 1983, 11(18);6301-18
[PubMed:6312418] [WorldCat.org] [DOI] (P p)

  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
Retrieved from "https://subtiwiki.uni-goettingen.de/wiki//index.php?title=Sandbox&oldid=88934"