Difference between revisions of "Sandbox"

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* '''Description:''' unknwon, similar to isochrismatase<br/><br/>
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* '''Description:''' 4.5 S 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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|''yaaI''
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|''scr''
 
|-
 
|-
 
|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''' || unknown
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|style="background:#ABCDEF;" align="center"| '''Product''' || small cytoplasmic RNA (scRNA, 4.5S RNA),
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|-
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|style="background:#ABCDEF;" align="center"|'''Function''' || unknown
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signal recognition particle-like (SRP) component
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|-
 
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|style="background:#ABCDEF;" align="center"| '''MW, pI''' || 20 kDa, 4.674 
 
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"| '''Gene length, protein length''' || 543 bp, 181 aa
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|style="background:#ABCDEF;" align="center"|'''Function''' || presecretory protein translocation
 
|-
 
|-
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaH]]'', ''[[yaaJ]]''
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|style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[yaaJ]]'', ''[[dnaX]]''
 
|-
 
|-
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yaaI_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_nucleotide.txt    Gene sequence      (+200bp)  ]'''  
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/yaaI_protein.txt Protein sequence]'''
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|style="background:#FAF8CC;" align="center"|'''[http://subtiwiki.uni-goettingen.de/scr_protein.txt Protein sequence]'''
 
|-
 
|-
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|colspan="2" | '''Genetic context''' <br/> [[Image:yaaI_context.gif]]
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|colspan="2" | '''Genetic context''' <br/> [[Image:scr_context.gif]]
 
|-
 
|-
 
|}
 
|}
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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+BG10081]
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* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG00095]
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=== Additional information===
 
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=The protein=
 
  
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=== Basic information/ Evolution ===
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* '''Structure:'''
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* '''Catalyzed reaction/ biological activity:'''
 
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* '''Protein family:'''
 
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* '''Paralogous protein(s):'''
 
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=== Extended information on the protein ===
 
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* '''Kinetic information:'''
 
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* '''Domains:'''
 
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* '''Modification:'''
 
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* '''Cofactor(s):'''
 
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* '''Effectors of protein activity:'''
 
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* '''Interactions:'''
 
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* '''Localization:'''
 
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=== Database entries ===
 
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* '''Structure:'''
 
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* '''Swiss prot entry:'''
 
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* '''KEGG entry:'''
 
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* '''E.C. number:'''
 
  
 
=== Additional information===
 
=== Additional information===
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−
important for survival of ethanol stress [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
 
  
 
=Expression and regulation=
 
=Expression and regulation=
  
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* '''Operon:'''  
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* '''Operon:''' ''[[yaaJ]]-[[scr]],  [[scr]]''
  
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* '''Sigma factor:''' [[SigB]] [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
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* '''Sigma factor:''' [[SigA]] (both promoters)
  
 
* '''Regulation:'''  
 
* '''Regulation:'''  
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* '''Regulatory mechanism:'''  
 
* '''Regulatory mechanism:'''  
  
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* '''Additional information:'''
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* '''Additional information:''' transcribed as 354 nt precursor, cleaved at the 5' end by [[rnc| RNase III]] and at the 3' site by [[rnjA| RNase J1]] to yield a 275 nt molecule, final trimming to 271 nt sc RNA by [[rph| RNase PH]] [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 PubMed]
  
 
=Biological materials =
 
=Biological materials =
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* '''lacZ fusion:'''
 
* '''lacZ fusion:'''
  
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* '''GFP fusion:'''
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=Labs working on this gene/protein=
  
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* '''two-hybrid system:'''
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[[David Bechhofer]], Mount Sinai School, New York, USA [http://www.mountsinai.org/Research/Centers%20Laboratories%20and%20Programs/Bechhofer%20Laboratory?citype=Physician&ciid=Bechhofer%20David%20H%201255565 Homepage]
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* '''Antibody:'''
 
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=Labs working on this gene/protein=
 
  
 
=Your additional remarks=
 
=Your additional remarks=
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=References=
 
=References=
  
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# Höper et al. (2005) Comprehensive characterization of the contribution of individual SigB-dependent general stress genes to stress resistance of ''Bacillus subtilis''.''J.Bacteriol.'' '''187:''' 2810-2826. [http://www.ncbi.nlm.nih.gov/sites/entrez/15805528 PubMed]
+
# Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of ''Bacillus subtilis'' small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. [http://www.ncbi.nlm.nih.gov/sites/entrez/17576666 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 13:45, 10 March 2009

  • Description: 4.5 S RNA

Gene name scr
Synonyms
Essential no
Product small cytoplasmic RNA (scRNA, 4.5S RNA),

signal recognition particle-like (SRP) component

Function presecretory protein translocation
Immediate neighbours yaaJ, dnaX
Gene sequence (+200bp) Protein sequence
Genetic context
Scr context.gif



The gene

Basic information

  • Coordinates:

Phenotypes of a mutant

Database entries

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

Additional information

Expression and regulation

  • Sigma factor: SigA (both promoters)
  • Regulation:
  • Regulatory mechanism:
  • Additional information: transcribed as 354 nt precursor, cleaved at the 5' end by RNase III and at the 3' site by RNase J1 to yield a 275 nt molecule, final trimming to 271 nt sc RNA by RNase PH PubMed

Biological materials

  • Mutant:
  • Expression vector:
  • lacZ fusion:

Labs working on this gene/protein

David Bechhofer, Mount Sinai School, New York, USA Homepage

Your additional remarks

References

  1. Yao, S., Blaustein, J. B. & Bechhofer, D. H. (2007). Processing of Bacillus subtilis small cytoplasmic RNA: evidence for an additional endonuclease cleavage site. Nucleic Acids Res. 35:4464-4473. PubMed
  2. Author1, Author2 & Author3 (year) Title Journal volume: page-page. PubMed
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