ybfE:Expression: Difference between revisions

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===Overview===
===Overview===
{{Expression_overview_placeholder}}
{{Expression_overview_placeholder}}
==Cellular Levels==
{{BacktoTop}}
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!|Molecule!!Organism or Strain!!Value!!Units!!Experimental Conditions!!Assay used!!Notes!!Reference(s)
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Protein
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''E. coli'' K-12 MG1655
|
960
|
molecules/cell/generation
|
*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
|-
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Protein
|
''E. coli'' K-12 MG1655
|
155
|
molecules/cell/generation
|
*Medium: MOPS Minimal 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
331
|
molecules/cell/generation
|
*Medium: MOPS Complete without Methionine 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
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===Notes===
==Transcription and Transcriptional Regulation==
==Transcription and Transcriptional Regulation==
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{{BacktoTop}}
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!Transcription unit(s)
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[[:Category:Txn_unit:ybfE|ybfE]]  
[[:Category:Txn_unit:ybfE|ybfE]]  
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<!--Transcription_notes--></protect>
<!--Transcription_notes--></protect>
===Notes===
===Notes===
{{Expression_transcription_placeholder}}
LexA-regulated <ref name='PMID:10760155'/>


==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
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{{BacktoTop}}
<protect>{{GBrowseFigureByCoord|711101|711141|ecoli|MG1655|Genes_unlabeled+DNA_unlabeled+flip|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:711101..711141
source=MG1655
flip=1
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
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===Notes===
===Notes===
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!Allele Name!!Mutation!!Phenotype!!Reference
!|Allele Name!!Mutation!!Phenotype!!Reference
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<big>'''Expression Studies'''</big>
<big>'''Expression Studies'''</big>
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!|Type!!Reference!!Notes
!|Type!!Reference!!Notes
|-  
|-  
|
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microarray  
microarray
|
|
[http://genexpdb.ou.edu/index.php?query=b0685 GenExpDB:b0685] ([[EcoliGenExpDB|EcoliWiki Page]])  
[[geoprofiles:b0685|GEO Profiles:b0685]] ([[Gene_Expression_Omnibus_%28GEO%29|EcoliWiki Page]])
|
|
Summary of data for ybfE from multiple microarray studies 
NCBI GEO profiles for ''ybfE''
|-  
|-  
|
|
microarray
microarray
|
|
[[geoprofiles:b0685|GEO Profiles:b0685]] ([[Gene_Expression_Omnibus_%28GEO%29|EcoliWiki Page]])
[http://genexpdb.ou.edu/index.php?query=b0685 GenExpDB:b0685] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
NCBI GEO profiles for ''ybfE''
Summary of data for ybfE from multiple microarray studies 


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<big>'''Expression Resources'''</big>
<big>'''Expression Resources'''</big>
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|- {{table heading style}}
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!|Resource Name!!Resource Type!!Description!!Source!!Notes
!|Resource Name!!Resource Type!!Description!!Source!!Notes
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[http://www.openbiosystems.com/GeneExpression/Non-Mammalian/Bacteria/EcoliPromoters/ OpenBioSystems][[Category:Genes in OpenBioSystems with Promoter Fusions]]
[http://www.openbiosystems.com/GeneExpression/Non-Mammalian/Bacteria/EcoliPromoters/ OpenBioSystems][[Category:Genes in OpenBioSystems with Promoter Fusions]]
|
|
GFP fusion described in Zaslaver, <i>et al.</i><br />Plate:109-AZ12; Well:E8<ref name="PMID:16862137" />  
GFP fusion described in Zaslaver, <i>et al.</i><br />Plate:109-AZ12; Well:E8<ref name="PMID: 16862137" />  


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<protect><!--Expression_experimental_notes--></protect>
<protect><!--Expression_experimental_notes--></protect>
===Notes===
===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11775 EcoCyc:EG11775] 
EcoCyc:EG11775
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1724 EchoBASE:EB1724] 
EchoBASE:EB1724
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://genexpdb.ou.edu/index.php?query=b0685 GenExpDB:b0685]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0685 EcoliGenExpDB:b0685]
|
|
   
   
|-
|-
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[[EcoGene]]
|
EcoGene:EG11775
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[RegulonDB]]
|
RegulonDB:ECK120001709
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[ASAP]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11775 EcoGene:EG11775] 
ASAP:ABE-0002335
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Accessions_notes--></protect>
<protect><!--Accessions_notes--></protect>
===Notes===
===Notes===
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<noinclude>
<noinclude>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
===Categories===
{{BacktoTop}}
{{BacktoTop}}
[[Category:Txn_unit:ybfE]]
[[Category:Txn_unit:ybfE]]

Latest revision as of 18:52, 21 July 2015

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Overview Transcription Translation Turnover Experimental Links References Suggestions

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MG1655

960

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[1]

Protein

E. coli K-12 MG1655

155

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[1]

Protein

E. coli K-12 MG1655

331

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID:24766808[1]

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

ybfE

edit table
Figure courtesy of RegulonDB


Notes

LexA-regulated [2]

Translation and Regulation of Translation

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<gbrowseImage> name=NC_000913:711101..711141 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.


Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b0685 (EcoliWiki Page)

NCBI GEO profiles for ybfE

microarray

GenExpDB:b0685 (EcoliWiki Page)

Summary of data for ybfE from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes

GFP Fusion

Intergenic region (711092..711277) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ12; Well:E8[3]

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<protect>

Notes

Accessions Related to ybfE Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:EG11775

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1724

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0685

EcoGene

EcoGene:EG11775

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001709

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002335

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.0 1.1 1.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 PubMed
  2. ↑ Fernández De Henestrosa, AR et al. (2000) Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol. Microbiol. 35 1560-72 PubMed
  3. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

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