Difference between revisions of "NcRNA"

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(Created page with "{{CategoryTree2 |Parents= * 6. Groups of genes |Neighbours= * 6.1. Ribosomal RNA * 6.2. tRNA * 6.3. ncRNA * 6.4. Short peptides * 6.5. [[GTP-binding proteins]...")
 
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* 6. [[Groups of genes]]
 
* 6. [[Groups of genes]]
 
|Neighbours=
 
|Neighbours=
−
* 6.1. [[Ribosomal RNA]]
+
* 6.1. [[Essential genes]]
−
* 6.2. [[tRNA]]
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* 6.2. [[Membrane proteins]]
−
* 6.3. [[ncRNA]]
+
* 6.3. [[GTP-binding proteins]]
−
* 6.4. [[Short peptides]]
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* 6.4. [[Phosphoproteins]]
−
* 6.5. [[GTP-binding proteins]]
+
* 6.5. [[Universally conserved proteins]]
−
* 6.6. [[Phosphoproteins]]
+
* 6.6. [[Poorly characterized/ putative enzymes]]
−
* 6.7. [[Universally conserved proteins]]
+
* 6.7. [[Proteins of unknown function]]
−
* 6.8. [[Membrane proteins]]
+
* 6.8. [[Short peptides]]
−
* 6.9. [[Essential genes]]
+
* 6.9. [[ncRNA]]
 
* 6.10. [[Pseudogenes]]
 
* 6.10. [[Pseudogenes]]
−
* 6.11. [[Poorly characterized/ putative enzymes]]
 
−
* 6.12. [[Proteins of unknown function]]
 
 
|Related=
 
|Related=
−
none
+
* [[RNA switch]]
 +
* [[RNase]]
 
|}}
 
|}}
 +
 +
__TOC__
 +
<br><br><br>
 +
'''6S RNA'''
 +
 +
* ''[[bsrA]]''
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* ''[[bsrB]]''
 +
 +
'''tmRNA'''
 +
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* ''[[ssrA]]''
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 +
'''small cytoplasmatic RNA (protein secretion)'''
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*''[[scr]]''
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'''RNA component of RNase P'''
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* ''[[rnpB]]''
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'''regulatory RNAs'''
 +
 +
* ''[[fsrA]]''
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* ''[[roxS]]''
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* ''[[rrcM]]''
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* [[sr1]]
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* [[SR4]]
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* [[RnaC]]
 +
 +
'''antisense RNAs of toxin/antitoxin systems'''
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* ''[[ratA]]''
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* ''[[as-bsrH]]''
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* ''[[as-yonT]]''
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* ''[[SR5]]''
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'''small RNAs with unknown functions'''
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* ''[[bsrC]]''
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* ''[[bsrD]]''
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* ''[[bsrF]]''
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* ''[[bsrH]]''
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* ''[[bsrI]]''
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* ''[[csfG]]''
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* ''[[surA]]'' (for ''[[yndL]]'')
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* ''[[surC]]''
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 +
'''Antisense RNAs were predicted for the following genes:''' {{PubMed|20525796}}
 +
* ''[[bglP]]''
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* ''[[comER]]''
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* ''[[ggaA]]''
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* ''[[jag]]''
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* ''[[leuA]]''
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* ''[[mbl]]''
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* ''[[mtlD]]''
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* ''[[mutS]]''
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* ''[[nadB]]''
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* ''[[ndoA]]''
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* ''[[opuBD]]''
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* ''[[sda]]''
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* ''[[sigA]]''
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* ''[[wprA]]''
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* ''[[yddR]]''
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* ''[[ydiF]]''
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* ''[[yfhD]]''
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* ''[[yndL]]'' (''[[surA]]'')
 +
* ''[[yoeA]]''
 +
* ''[[yoqZ]]''
 +
* ''[[yqzJ]]''
 +
* ''[[ytoA]]''
 +
* ''[[ytoI]]''
 +
* ''[[ywfM]]''
 +
* ''[[ywqA]]''
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* ''[[yyaQ]]''
 +
 +
'''Additional noncoding RNAs were predicted for the following intergenic regions:''' {{PubMed|20525796}}
 +
* ''[[yqaJ]]''-''[[yqaI]]''
 +
* ''[[yqaO]]''-''[[yqaN]]''
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* ''[[yndN]]''-''[[lexA]]''
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* ''[[ydcO]]''-''[[ydcP]]''
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* ''[[yolA]]''-''[[yokL]]''
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* ''[[yokC]]''-''[[yokB]]''
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* ''[[pbpG]]''-''[[ywhD]]''
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* ''[[stoA]]''-''[[zosA]]''
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* ''[[yobI]]''-''[[yobJ]]''
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* ''[[vmlR]]''-''[[ydgF]]''
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* ''[[yrzI]]''-''[[yrhG]]''
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* ''[[yfmI]]''-''[[yfmG]]''
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* ''[[hxlR]]''-''[[srfAA]]''
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* ''[[mutL]]''-''[[ymzD]]''
 +
* ''[[mntA]]''-''[[menC]]''
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* ''[[yopM]]''-''[[yopL]]''
 +
* ''[[yizD]]''-''[[yjbH]]''
 +
* ''[[pps]]''-''[[xynA]]''
 +
* ''[[yqdB]]''-''[[yqbM]]''
 +
* ''[[yugI]]''-''[[alaT]]''
 +
* ''[[trxA]]''-''[[xsa]]''
 +
* ''[[ykwD]]''-''[[pbpH]]''
 +
* ''[[ymzA]]''-''[[nrdI]]''
 +
* ''[[yvcI]]''-''[[trxB]]''
 +
* ''[[glmM]]''-''[[glmS]]''
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* ''[[yhaZ]]''-''[[yhaX]]''
 +
* ''[[yneK]]''-''[[cotM]]''
 +
* ''[[trpS]]''-''[[oppA]]''
 +
* ''[[gerPA]]''-''[[yisI]]''
 +
 +
==Reviews==
 +
<pubmed> 19239884 19207102 20525796 19859665 21646430 22827307 24576839 25808661 27784798</pubmed>
 +
 +
==Important original publications==
 +
<pubmed>22383849</pubmed>
 +
=Back to [[categories]]=

Latest revision as of 15:40, 28 October 2016

Parent category
Neighbouring categories
Related categories




6S RNA

tmRNA

small cytoplasmatic RNA (protein secretion)

RNA component of RNase P

regulatory RNAs

antisense RNAs of toxin/antitoxin systems

small RNAs with unknown functions

Antisense RNAs were predicted for the following genes: PubMed

Additional noncoding RNAs were predicted for the following intergenic regions: PubMed

Reviews

Ruben A T Mars, Pierre Nicolas, Emma L Denham, Jan Maarten van Dijl
Regulatory RNAs in Bacillus subtilis: a Gram-Positive Perspective on Bacterial RNA-Mediated Regulation of Gene Expression.
Microbiol Mol Biol Rev: 2016, 80(4);1029-1057
[PubMed:27784798] [WorldCat.org] [DOI] (I e)

Sabine Brantl, Natalie Jahn
sRNAs in bacterial type I and type III toxin-antitoxin systems.
FEMS Microbiol Rev: 2015, 39(3);413-27
[PubMed:25808661] [WorldCat.org] [DOI] (I p)

Sabine Brantl, Reinhold Brückner
Small regulatory RNAs from low-GC Gram-positive bacteria.
RNA Biol: 2014, 11(5);443-56
[PubMed:24576839] [WorldCat.org] [DOI] (I p)

Sabine Brantl
Acting antisense: plasmid- and chromosome-encoded sRNAs from Gram-positive bacteria.
Future Microbiol: 2012, 7(7);853-71
[PubMed:22827307] [WorldCat.org] [DOI] (I p)

Jens Georg, Wolfgang R Hess
cis-antisense RNA, another level of gene regulation in bacteria.
Microbiol Mol Biol Rev: 2011, 75(2);286-300
[PubMed:21646430] [WorldCat.org] [DOI] (I p)

Irnov Irnov, Cynthia M Sharma, Jörg Vogel, Wade C Winkler
Identification of regulatory RNAs in Bacillus subtilis.
Nucleic Acids Res: 2010, 38(19);6637-51
[PubMed:20525796] [WorldCat.org] [DOI] (I p)

Pascale Romby, Emmanuelle Charpentier
An overview of RNAs with regulatory functions in gram-positive bacteria.
Cell Mol Life Sci: 2010, 67(2);217-37
[PubMed:19859665] [WorldCat.org] [DOI] (I p)

Lauren S Waters, Gisela Storz
Regulatory RNAs in bacteria.
Cell: 2009, 136(4);615-28
[PubMed:19239884] [WorldCat.org] [DOI] (I p)

Sabine Brantl
Bacterial chromosome-encoded small regulatory RNAs.
Future Microbiol: 2009, 4(1);85-103
[PubMed:19207102] [WorldCat.org] [DOI] (I p)


Important original publications

Pierre Nicolas, Ulrike Mäder, Etienne Dervyn, Tatiana Rochat, Aurélie Leduc, Nathalie Pigeonneau, Elena Bidnenko, Elodie Marchadier, Mark Hoebeke, Stéphane Aymerich, Dörte Becher, Paola Bisicchia, Eric Botella, Olivier Delumeau, Geoff Doherty, Emma L Denham, Mark J Fogg, Vincent Fromion, Anne Goelzer, Annette Hansen, Elisabeth Härtig, Colin R Harwood, Georg Homuth, Hanne Jarmer, Matthieu Jules, Edda Klipp, Ludovic Le Chat, François Lecointe, Peter Lewis, Wolfram Liebermeister, Anika March, Ruben A T Mars, Priyanka Nannapaneni, David Noone, Susanne Pohl, Bernd Rinn, Frank Rügheimer, Praveen K Sappa, Franck Samson, Marc Schaffer, Benno Schwikowski, Leif Steil, Jörg Stülke, Thomas Wiegert, Kevin M Devine, Anthony J Wilkinson, Jan Maarten van Dijl, Michael Hecker, Uwe Völker, Philippe Bessières, Philippe Noirot
Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis.
Science: 2012, 335(6072);1103-6
[PubMed:22383849] [WorldCat.org] [DOI] (I p)

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