yceD:Expression: Difference between revisions

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{{Tab|Quickview|yceD}}{{Tab|Gene|yceD}}{{Tab|Gene Product(s)|yceD}}{{Tab On|Expression|yceD}}{{Tab|Evolution|yceD}}{{Tab|On One Page|yceD}}{{TabsBottom}}
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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
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</noinclude>[[Category:Txn_unit:yceD-rpmF]]
</noinclude>
==Overview==
===Overview===
{{Expression_overview_placeholder}}
{{Expression_overview_placeholder}}
==Cellular Levels==
{{BacktoTop}}
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|- align='left' bgcolor='#CCCCFF'
!|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
|
42.904+/-0.332
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
|
Single Molecule Fluorescence
|
PMID:20671182
|-
|
mRNA
|
Ecoli K-12
|
1.546065259
|
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
|
5980
|
molecules/cell/generation
|
*Medium: MOPS Complete 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
|
PMID: 24766808
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
1290
|
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
|
3051
|
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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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.35289.F49c03b89cade2-->
===Notes===
==Transcription and Transcriptional Regulation==
==Transcription and Transcriptional Regulation==
{{BacktoTop}}
<protect>
<protect>
{|{{Prettytable}}
{|{{Prettytable}}
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|-
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!Transcription unit(s)
!|Transcription unit(s)
|-
|-  
|
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[[:Category:Txn_unit:yceD-rpmF|yceD-rpmF]]  
[[:Category:Txn_unit:yceD-rpmF|yceD-rpmF]]  
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{{expression_transcription_help}}
 
<!--Transcription_notes--></protect>
<!--Transcription_notes--></protect>
===Notes===
===Notes===
Line 39: Line 204:


==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
<protect>{{GBrowseFigureByCoord|1146002|1146032|ecoli|MG1655|GenesNew+DNA}}
{{BacktoTop}}
{{Expression_translation_help}}
<protect><gbrowseImage>
name=NC_000913:1145997..1146037
source=MG1655
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
{{Nterm_closeup}}
 
<!--Translation_notes--></protect>
<!--Translation_notes--></protect>
===Notes===
{{Expression_translation_placeholder}}
{{Expression_translation_placeholder}}


==Turnover and Regulation of Turnover==
==Turnover and Regulation of Turnover==
<!--Turnover_notes--></protect>
===Notes===
{{Expression_turnover_placeholder}}
{{Expression_turnover_placeholder}}


==Experimental==
==Experimental==
{{BacktoTop}}
<protect>
<protect>
===Mutations Affecting Expression===
<big>'''Mutations Affecting Expression'''</big>
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===Expression Studies===
 
<!--box uid=421aa90e079fa326b6494f812ad13e79..T46a042a05371b-->
<big>'''Expression Studies'''</big>
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|
microarray
|
[[geoprofiles:b1088|GEO Profiles:b1088]] ([[Gene_Expression_Omnibus_%28GEO%29|EcoliWiki Page]])
|
NCBI GEO profiles for ''yceD''
|-
|
microarray
|
[http://genexpdb.ou.edu/index.php?query=b1088 GenExpDB:b1088] ([[EcoliGenExpDB|EcoliWiki Page]])
|
Summary of data for yceD from multiple microarray studies 
 
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===Expression Resources===
 
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<big>'''Expression Resources'''</big>
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!|Resource Name!!Resource Type!!Description!!Source!!Notes
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<protect><!--Expression_experimental_notes--></protect>
<protect><!--Expression_experimental_notes--></protect>
===Notes===
===Notes===




==Accessions Related to yceD Expression==
==Accessions Related to ''yceD'' Expression==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11119 EcoCyc:EG11119] 
EcoCyc:EG11119
|
|
''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=EB1109 EchoBASE:EB1109] 
EchoBASE:EB1109
|
|
''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://chase.ou.edu/macro/searchlink.php?bnum=b1088 EcoliGenExpDB:b1088]
[http://chase.ou.edu/macro/searchlink.php?bnum=b1088 EcoliGenExpDB:b1088]
|
|
   
   
|-
|-
|
[[EcoGene]]
|
EcoGene:EG11119
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001103
|
''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=EG11119 EcoGene:EG11119] 
ASAP:ABE-0003684
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<protect><!--Accessions_notes--></protect>
<protect><!--Accessions_notes--></protect>
===Notes===
===Notes===
{{EXPRESSION_ACCESSIONS_NOTES}}
 


==Links==
==Links==
{{BacktoTop}}
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<noinclude>
<noinclude>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</noinclude>
===Categories===
{{BacktoTop}}
[[Category:Txn_unit:yceD-rpmF]]

Latest revision as of 18:49, 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

42.904+/-0.332

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182[2]

mRNA

Ecoli K-12

1.546065259

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

5980

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

1290

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

3051

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

[back to top]


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

Transcription unit(s)

yceD-rpmF

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_000913:1145997..1146037 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

[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:b1088 (EcoliWiki Page)

NCBI GEO profiles for yceD

microarray

GenExpDB:b1088 (EcoliWiki Page)

Summary of data for yceD 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 yceD Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11119

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1109

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1088

EcoGene

EcoGene:EG11119

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001103

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003684

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

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References

[back to top]


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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