yidC:Expression: Difference between revisions

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****************************************************************************************** -->{{Help Cellular levels}}
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{|   id="B49c03f3678b97"  class=" tableEdit MoleculesPerCellTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B49c03f3678b97"  class=" tableEdit MoleculesPerCellTable"   
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!|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)
|-
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Protein
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''E. coli'' K-12 MC4100
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7.04E+02
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molecules/cell
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*Medium:  median data from rich and minimal media
*Temperature (°C):  37
*Doubling time (min): Growth Rate(min): 
*Growth phase: other:
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emPAI
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PMID:18304323
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Protein
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''E. coli'' K-12 MG1655
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8807
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molecules/cell/generation
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*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
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Ribosome Profiling
|
 
|
PMID: 24766808
|-
|
Protein
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''E. coli'' K-12 MG1655
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1094
|
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
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2589
 
|
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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!|Transcription unit(s)
!|Transcription unit(s)


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==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
{{BacktoTop}}
{{BacktoTop}}
<protect>{{GBrowseFigureByCoord|3883079|3883119|ecoli|MG1655|Gene+DNA_+Protein|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:3883079..3883119
source=MG1655
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
{{Nterm_closeup}}
 
<!--Translation_notes--></protect>
<!--Translation_notes--></protect>
===Notes===
===Notes===
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{|   id="M46ab810617b10"  class=" tableEdit Expression_allele_table"   
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!|Allele Name!!Mutation!!Phenotype!!Reference
!|Allele Name!!Mutation!!Phenotype!!Reference


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!|Type!!Reference!!Notes
!|Type!!Reference!!Notes
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microarray  
microarray
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[http://genexpdb.ou.edu/index.php?query=b3705 GenExpDB:b3705] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://genexpdb.ou.edu/index.php?query=b3705 GenExpDB:b3705] ([[EcoliGenExpDB|EcoliWiki Page]])  
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!|Resource Name!!Resource Type!!Description!!Source!!Notes
!|Resource Name!!Resource Type!!Description!!Source!!Notes
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11197 EcoCyc:EG11197]
EcoCyc:EG11197
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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=EB1183 EchoBASE:EB1183]
EchoBASE:EB1183
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
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EcoGene:EG11197
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11197 EcoGene:EG11197]
[[RegulonDB]]
|
|
RegulonDB:ECK120001178
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[ASAP]]
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ASAP:ABE-0012120
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments


Latest revision as of 18:32, 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

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See Help:Cellular levels

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

Protein

E. coli K-12 MC4100

7.04E+02

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

E. coli K-12 MG1655

8807

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[2]

Protein

E. coli K-12 MG1655

1094

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[2]

Protein

E. coli K-12 MG1655

2589

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[2]

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)
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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

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<gbrowseImage> name=NC_000913:3883079..3883119 source=MG1655 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:b3705 (EcoliWiki Page)

NCBI GEO profiles for yidC

microarray

GenExpDB:b3705 (EcoliWiki Page)

Summary of data for yidC 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 (3882402..3882756) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ18; Well:E12[3]

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<protect>

Notes

Accessions Related to yidC Expression

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

Database Accession Notes

EcoCyc

EcoCyc:EG11197

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1183

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3705

EcoGene

EcoGene:EG11197

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001178

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012120

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. ↑ Ishihama, Y et al. (2008) Protein abundance profiling of the Escherichia coli cytosol. BMC Genomics 9 102 PubMed
  2. ↑ 2.0 2.1 2.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 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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