ygfB:Expression: Difference between revisions

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*  
*  
****************************************************************************************** -->{{Help Cellular levels}}
****************************************************************************************** -->{{Help Cellular levels}}
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|- align='left' bgcolor='#CCCCFF'
!|Molecule!!Organism or Strain!!Cellular level!!Units!!Medium!!Temperature °C!!Other (e.g. anaerobic)!!Growth rate!!Assay used!!Notes!!Reference(s)
!|Molecule!!Organism or Strain!!Value!!Units!!Experimental Conditions!!Assay used!!Notes!!Reference(s)
|-
|
Protein
|
''E. coli'' K-12 MC4100
|
1.04E+03
|
molecules/cell
|
*Medium:  median data from rich and minimal media
*Temperature (°C):  37
*Doubling time (min): Growth Rate(min): 
*Growth phase: other:
|
emPAI
|
 
|
PMID:18304323
|-
|
Protein
|
Ecoli K-12
|
42.661+/-0.481
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
 
|
Single Molecule Fluorescence
|
PMID:20671182
|-
|
mRNA
|
Ecoli K-12
|
0.160034602
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
 
|
by RNA_Seq
|
PMID:20671182
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
2535
|
molecules/cell/generation
|
*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|


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PMID: 24766808
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Protein
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''E. coli'' K-12 MG1655
|
878
|
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
|
1707
 
|
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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****************************************************************************************** -->{{expression_transcription_help}}
****************************************************************************************** -->{{expression_transcription_help}}
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!|Transcription unit(s)
!|Transcription unit(s)
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[[:Category:Txn_unit:visC|visC]]  
[[:Category:Txn_unit:visC|visC]]  


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==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
{{BacktoTop}}
{{BacktoTop}}
<protect>{{GBrowseFigureByCoord|3053446|3053486|ecoli|MG1655|Genes_unlabeled+DNA_unlabeled+flip|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:3053446..3053486
source=MG1655
flip=1
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
{{Nterm_closeup}}
 
<!--Translation_notes--></protect>
<!--Translation_notes--></protect>
===Notes===
===Notes===
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****************************************************************************************** -->{{Expression_allele_table_help}}
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!|Allele Name!!Mutation!!Phenotype!!Reference
!|Allele Name!!Mutation!!Phenotype!!Reference


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|- {{table heading style}}
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!|Type!!Reference!!Notes
!|Type!!Reference!!Notes
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|-  
|-  
|
|
microarray  
microarray
|
|
[http://genexpdb.ou.edu/index.php?query=b2909 GenExpDB:b2909] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://genexpdb.ou.edu/index.php?query=b2909 GenExpDB:b2909] ([[EcoliGenExpDB|EcoliWiki Page]])  
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Summary of data for ygfB from multiple microarray studies   
Summary of data for ygfB from multiple microarray studies   


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****************************************************************************************** -->{{Expression_resource_table_help}}
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!|Resource Name!!Resource Type!!Description!!Source!!Notes
!|Resource Name!!Resource Type!!Description!!Source!!Notes


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****************************************************************************************** -->{{Gene_accessions_help}}
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11323 EcoCyc:EG11323]
EcoCyc:EG11323
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1299 EchoBASE:EB1299]
EchoBASE:EB1299
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
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|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
EcoGene:EG11323
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11323 EcoGene:EG11323]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[RegulonDB]]
|
RegulonDB:ECK120001294
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[ASAP]]
|
ASAP:ABE-0009551
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 18:37, 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 MC4100

1.04E+03

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323[1]

Protein

Ecoli K-12

42.661+/-0.481

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

Single Molecule Fluorescence

PMID:20671182[2]

mRNA

Ecoli K-12

0.160034602

Molecules/cell

  • Medium:
  • Temperature (°C):
  • Doubling time (min): Growth Rate(min): *
  • Growth phase: other: *

by RNA_Seq

PMID:20671182[2]

Protein

E. coli K-12 MG1655

2535

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[3]

Protein

E. coli K-12 MG1655

878

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[3]

Protein

E. coli K-12 MG1655

1707

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[3]

edit table

Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

visC

edit table
Figure courtesy of RegulonDB


Notes

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

Translation and Regulation of Translation

[back to top]


<gbrowseImage> name=NC_000913:3053446..3053486 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

[back to top]


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

Allele Name Mutation Phenotype Reference
edit table


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

Type Reference Notes

microarray

GEO Profiles:b2909 (EcoliWiki Page)

NCBI GEO profiles for ygfB

microarray

GenExpDB:b2909 (EcoliWiki Page)

Summary of data for ygfB 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
edit table

<protect>

Notes

Accessions Related to ygfB Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11323

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1299

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2909

EcoGene

EcoGene:EG11323

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001294

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009551

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

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References

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

  1. ↑ Ishihama, Y et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9 102 PubMed
  2. ↑ 2.0 2.1 Taniguchi, Y et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329 533-8 PubMed
  3. ↑ 3.0 3.1 3.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 PubMed

Categories

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