Difference between revisions of "Sandbox"

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* '''Description:''' 6S RNA<br/><br/>
+
* '''Description:''' small RNA <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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|''bsrA''
+
|''bsrD''
 
|-
 
|-
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
 
|style="background:#ABCDEF;" align="center"| '''Synonyms''' || '' ''
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|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|style="background:#ABCDEF;" align="center"| '''Essential''' || no  
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Product''' || 6S RNA
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|style="background:#ABCDEF;" align="center"| '''Product''' || small RNA
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || antagonist of [[SigA]]
+
|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  190 bp
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|style="background:#ABCDEF;" align="center"| '''Gene length''' ||  bp
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yrvM]]'', ''[[aspS]]''
+
|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yddM]]'', ''[[yddN]]''
 
|-
 
|-
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
 
|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/genE.txt    Gene sequence      (+200bp)  ]'''  
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:BsrA_context.jpeg]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:genE_context.gif]]
 +
<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 
|-
 
|-
 
|}
 
|}
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===Phenotypes of a mutant ===
 
===Phenotypes of a mutant ===
−
 
−
reduced growth rate  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
 
−
 
  
 
=== Database entries ===
 
=== Database entries ===
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=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:''' ''bsrA''  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Operon:'''  
  
−
* '''Sigma factor:''' [[SigA]]  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Sigma factor:'''  
  
−
* '''Regulation:''' expressed in vegetative cells  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Regulation:'''  
  
 
* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
−
* '''Additional information:''' transcribed as 201 nt RNA, processed to mature 190 bp 6S RNA  [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
* '''Additional information:'''  
  
 
=Biological materials =
 
=Biological materials =
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=References=
 
=References=
  
−
<pubmed>12177353 15811922, </pubmed>
+
<pubmed>18948176, </pubmed>
−
# Suzuma S, Asari S, Bunai K, Yoshino K, Ando Y, Kakeshita H, Fujita M, Nakamura K, Yamane K (2002) Identification and characterization of novel small RNAs in the ''aspS-yrvM'' intergenic region of the ''Bacillus subtilis'' genome.. ''Microbiology'' '''148:''' 2591-2598. [http://www.ncbi.nlm.nih.gov/sites/entrez/12177353 PubMed]
+
# Saito S, Kakeshita H, Nakamura K (2009) Novel small RNA-encoding genes in the intergenic regions of ''Bacillus subtilis''. ''Gene'' '''428:''' 2-8. [http://www.ncbi.nlm.nih.gov/sites/entrez/18948176 PubMed]
−
# Barrick JE, Sudarsan N, Weinberg Z, Ruzzo WL, Breaker RR(2005) 6S RNA is a widespread regulator of eubacterial RNA polymerase that resembles an open promoter.''RNA'' '''11:''' 774-784. [http://www.ncbi.nlm.nih.gov/sites/entrez/15811922 PubMed]
 
−
# Author1, Author2 & Author3 (year) Title ''Journal'' '''volume:''' page-page. [http://www.ncbi.nlm.nih.gov/sites/entrez/PMID PubMed]
 

Revision as of 13:10, 8 June 2009

  • Description: small RNA

Gene name bsrD
Synonyms
Essential no
Product small RNA
Function unknown
Gene length bp
Immediate neighbours yddM, yddN
Gene sequence (+200bp)
Genetic context
File:GenE 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: no entry
  • Structure:

Additional information

Expression and regulation

  • Operon:
  • Sigma factor:
  • Regulation:
  • Regulatory mechanism:
  • Additional information:

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:


Labs working on this gene/RNA

Kouji Nakamura, Tsukuba, University, Japan

Your additional remarks

References

Shinichi Saito, Hiroshi Kakeshita, Kouji Nakamura
Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis.
Gene: 2009, 428(1-2);2-8
[PubMed:18948176] [WorldCat.org] [DOI] (P p)

  1. Saito S, Kakeshita H, Nakamura K (2009) Novel small RNA-encoding genes in the intergenic regions of Bacillus subtilis. Gene 428: 2-8. PubMed
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