RnjB - Revision history

Jstuelk: Replaced content with "{{#bank: rnjB}}"

2015-09-16T09:34:02Z

Replaced content with "{{#bank: rnjB}}"

Jstuelk: /* Biological materials */

2015-01-05T12:26:45Z

‎Biological materials

134.76.70.252 at 09:40, 17 April 2014

2014-04-17T09:40:45Z

134.76.38.147 at 13:46, 2 April 2014

2014-04-02T13:46:19Z

134.76.70.252 at 14:16, 18 November 2013

2013-11-18T14:16:51Z

Jstuelk at 17:18, 13 November 2013

2013-11-13T17:18:23Z

Jstuelk: /* References */

2013-07-13T16:21:17Z

‎References

134.76.70.252 at 13:24, 16 May 2013

2013-05-16T13:24:47Z

134.76.70.252 at 10:16, 14 May 2013

2013-05-14T10:16:49Z

134.76.70.252 at 12:52, 13 May 2013

2013-05-13T12:52:42Z

← Older revision		Revision as of 09:34, 16 September 2015
Line 1:		Line 1:
−	* '''Description:''' [[RNase]] J2<br/><br/>	+	{{#bank: rnjB}}
−
−	{~~\| align="right" border="1" cellpadding="2"~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Gene name'''~~
−	~~\|''rnjB ''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Synonyms''' \|\| ''ymfA''~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Essential''' \|\| no~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Product''' \|\| [[RNase]] J2~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Function''' \|\| RNA processing and degradation~~
−	\|-
−	~~\|colspan="2" style="background:~~#~~FAF8CC;" align="center"\| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http~~:~~//subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16780~~ rnjB]
−	\|-
−	\|colspan="2" style="background:#FAF8CC;" align="center"\| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RnjB RNase J2]
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''MW, pI''' \|\| 56 kDa, 9.18~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\| '''Gene length, protein length''' \|\| 1545 bp, 515 aa~~
−	\|-
−	~~\|style="background:#ABCDEF;" align="center"\|'''Immediate neighbours''' \|\| ''[[dapA]]'', ''[[tepA]]''~~
−	\|-
−	\|style="background:#FAF8CC;" align="center"\|'''Sequences'''\|\|[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16780 DNA_with_flanks]
−	\|-
−	\|-
−	\|-
−	~~\|colspan="2" \| '''Genetic context''' <br/> [[Image:ymfA_context.gif]]~~
−	~~<div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>~~
−	\|-
−	\|colspan="2" \|'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnjB_1749418_1751085_1 Expression at a glance]'''   {{PubMed\|22383849}}<br/>[[Image:rnjB_expression.png\|500px\|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16780]]
−	\|-
−	\|}
−
−	~~__TOC__~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/><br/><br/>~~
−	~~<br/><br/>~~
−
−	~~= [[Categories]] containing this gene/protein =~~
−	~~{{SubtiWiki category\|[[Rnases]]~~}}
−
−	~~= This gene is a member of the following [[regulons]] =~~
−
−
−	~~=The gene=~~
−
−	~~=== Basic information ===~~
−
−	* '''Locus tag:''' BSU16780
−
−	~~===Phenotypes of a mutant ===~~
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16780&redirect=T BSU16780]
−
−	* '''DBTBS entry:''' no entry
−
−	* '''SubtiList entry:''' [http://genolist.pasteur.fr/SubtiList/genome.cgi?gene_detail+BG13422]
−
−	~~=== Additional information===~~
−
−	~~=The protein=~~
−
−	~~=== Basic information/ Evolution ===~~
−
−	* '''Catalyzed reaction/ biological activity:''' endoribonuclease, involved in processing of ''[[thrS]]'' mRNA
−
−	* '''Protein family:''' [[RNase]] J subfamily (according to Swiss-Prot)
−
−	* '''Paralogous protein(s):''' [[RnjA]]
−
−	~~=== Extended information on the protein ===~~
−
−	* '''Kinetic information:'''
−
−	* '''Domains:'''
−
−	* '''Modification:'''
−
−	* '''Cofactor(s):'''
−
−	* '''Effectors of protein activity:'''
−
−	* '''[[SubtInteract\|Interactions]]:'''
−	** associated to the [[RNA degradosome]] {{PubMed\|19193632}}
−	** [[RnjA]]-[[RnjB]] {{PubMed\|19193632,20025672}}
−
−	* '''[[Localization]]:''' cytoplasm (according to Swiss-Prot)
−
−	~~=== Database entries ===~~
−	* '''BsubCyc:''' [http://bsubcyc.org/BSUB/NEW-IMAGE?type=NIL&object=BSU16780&redirect=T BSU16780]
−
−	* '''Structure:''' [http://www.rcsb.org/pdb/explore/explore.do?structureId=3ZQ4 3ZQ4] (RNase J1) {{PubMed\|21893285}}
−
−	* '''KEGG entry:''' [http://www.genome.jp/dbget-bin/www_bget?bsu:BSU16780]
−
−	* '''E.C. number:'''
−
−	~~=== Additional information===~~
−
−	~~=Expression and regulation=~~
−
−	* '''Operon:''' ''[[rnjB]]'' {{PubMed\|24187087}}
−
−	* '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnjB_1749418_1751085_1 rnjB] {{PubMed\|22383849}}
−
−	* '''[[Sigma factor]]:''' [[SigA]] {{PubMed\|24187087}}
−
−	* '''Regulation:''' constitutive expression {{PubMed\|24187087}}
−
−	* '''Regulatory mechanism:'''
−
−	* '''Additional information:'''
−	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1201 {{PubMed\|24696501}}
−	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3208 {{PubMed\|24696501}}
−
−	~~=Biological materials =~~
−
−	* '''Mutant:''' GP1113 (miniTn10 spc), available in [[Stülke]] lab
−
−	* '''Expression vector:'''
−
−	* '''lacZ fusion:''' pGP419 (in [[pAC7]]), available in [[Stülke]] lab
−
−	* '''GFP fusion:'''
−
−	* '''two-hybrid system:''' B. pertussis adenylate cyclase-based bacterial two hybrid system ([[BACTH]]), available in [[Stülke]] lab
−
−	* '''FLAG-tag construct:''' GP1001 (spc, based on [[pGP1331]]), available in the [[Stülke]] lab
−
−	* '''Antibody:'''
−
−	~~=Labs working on this gene/protein=~~
−
−	~~[[Harald Putzer]], IBPC Paris, France [http://www.ibpc.fr/UPR9073/putzer/recherches_harald.htm Homepage]~~
−
−	~~=Your additional remarks=~~
−
−	~~=References=~~
−	~~==Reviews==~~
−	~~<pubmed>20458164 21893280 23403287,21957024 22568516 </pubmed>~~
−
−	~~==Original publications==~~
−	~~<pubmed>15831787 18204464 18713320 19193632, 19633085 20025672 21862575 21893285 24187087 </pubmed>~~
−
−	~~[[Category:Protein-coding genes]]~~

@@ Line 121: / Line 121: @@
 =Biological materials =
-* '''Mutant:''' GP45 (spc), GP1113 (miniTn10 spc), both available in [[Stülke]] lab
+* '''Mutant:''' GP1113 (miniTn10 spc), available in [[Stülke]] lab
 * '''Expression vector:'''

← Older revision		Revision as of 09:40, 17 April 2014
Line 116:		Line 116:

	* '''Additional information:'''		* '''Additional information:'''
		+	** number of protein molecules per cell (minimal medium with glucose and ammonium): 1201 {{PubMed\|24696501}}
		+	** number of protein molecules per cell (complex medium with amino acids, without glucose): 3208 {{PubMed\|24696501}}

	=Biological materials =		=Biological materials =

@@ Line 56: / Line 56: @@
 === Database entries ===
 * '''DBTBS entry:''' no entry
@@ Line 92: / Line 93: @@
 === Database entries ===
 * '''Structure:'''	[http://www.rcsb.org/pdb/explore/explore.do?structureId=3ZQ4 3ZQ4] (RNase J1) {{PubMed|21893285}}

@@ Line 16: / Line 16: @@
 |colspan="2" style="background:#FAF8CC;" align="center"| '''Gene expression levels in [http://subtiwiki.uni-goettingen.de/apps/expression/ ''Subti''Express]''': [http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16780 rnjB]
 |-
-|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://cellpublisher.gobics.de/subtinteract/startpage/start/ ''Subt''Interact]''': [http://cellpublisher.gobics.de/subtinteract/interactionList/2/RnjB RNase J2]
+|colspan="2" style="background:#FAF8CC;" align="center"| '''Interactions involving this protein in [http://subtiwiki.uni-goettingen.de/interact/ ''Subt''Interact]''': [http://subtiwiki.uni-goettingen.de/interact/index.php?protein=RnjB RNase J2]
 |-
 |style="background:#ABCDEF;" align="center"| '''MW, pI''' || 56 kDa, 9.18

@@ Line 103: / Line 103: @@
 =Expression and regulation=
-* '''Operon:'''
+* '''Operon:''' ''[[rnjB]]'' {{PubMed|24187087}}
 * '''Expression browser:''' [http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnjB_1749418_1751085_1 rnjB] {{PubMed|22383849}}
-* '''[[Sigma factor]]:'''
+* '''[[Sigma factor]]:''' [[SigA]] {{PubMed|24187087}}
-* '''Regulation:'''
+* '''Regulation:''' constitutive expression {{PubMed|24187087}}
 * '''Regulatory mechanism:'''
@@ Line 142: / Line 142: @@
 ==Original publications==
-<pubmed>15831787 18204464 18713320 19193632, 19633085 20025672 21862575 21893285</pubmed>
+<pubmed>15831787 18204464 18713320 19193632, 19633085 20025672 21862575 21893285 24187087 </pubmed>
 [[Category:Protein-coding genes]]

@@ Line 139: / Line 139: @@
 =References=
 ==Reviews==
-'''Additional reviews:''' {{PubMed|23403287,21957024}}
+<pubmed>20458164 21893280 23403287,21957024 22568516 </pubmed>
 ==Original publications==
-'''Additional publications:''' {{PubMed|21893285}}
+<pubmed>15831787 18204464 18713320 19193632, 19633085 20025672 21862575 21893285</pubmed>
 [[Category:Protein-coding genes]]

@@ Line 31: / Line 31: @@
   <div align="right"> <small>This image was kindly provided by [http://genolist.pasteur.fr/SubtiList/ SubtiList]</small></div>
 |-
-|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnjB_1749418_1751085_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rnjB_expression.png|500px]]
+|colspan="2" |'''[http://genome.jouy.inra.fr/cgi-bin/seb/viewdetail.py?id=rnjB_1749418_1751085_1 Expression at a glance]'''&#160;&#160;&#160;{{PubMed|22383849}}<br/>[[Image:rnjB_expression.png|500px|link=http://subtiwiki.uni-goettingen.de/apps/expression/expression.php?search=BSU16780]]
 |-
 |}

@@ Line 24: / Line 24: @@
 |style="background:#ABCDEF;" align="center"|'''Immediate neighbours''' || ''[[dapA]]'', ''[[tepA]]''
 |-
-|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16780 Advanced_DNA]
+|style="background:#FAF8CC;" align="center"|'''Sequences'''||[http://bsubcyc.org/BSUB/sequence-aa?type=GENE&object=BSU16780 Protein] [http://bsubcyc.org/BSUB/sequence?type=GENE&object=BSU16780 DNA] [http://bsubcyc.org/BSUB/seq-selector?chromosome=CHROM-1&object=BSU16780 DNA_with_flanks]
 |-
 |-