atpD:Expression: Difference between revisions

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<noinclude>{{TabsTop}}
{{Tab|Quickview|atpD}}{{Tab|Gene|atpD}}{{Tab|Gene Product(s)|atpD}}{{Tab On|Expression|atpD}}{{Tab|Evolution|atpD}}{{Tab|On One Page|atpD}}{{TabsBottom}}
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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
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</noinclude>[[Category:Txn_unit:atpBEFHAGDC]]
</noinclude>
==Overview==
===Overview===
{{Expression_overview_placeholder}}
{{Expression_overview_placeholder}}
==Cellular Levels==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="C49c01dc780cd6"  class=" tableEdit MoleculesPerCellTable" 
|- align='left' bgcolor='#CCCCFF'
!|Molecule!!Organism or Strain!!Value!!Units!!Experimental Conditions!!Assay used!!Notes!!Reference(s)
|-
|
Protein
|
''E. coli'' K-12 MC4100
|
3.11E+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
|
685.856+/-3.117
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
|
Single Molecule Fluorescence
|
PMID:20671182
|-
|
mRNA
|
Ecoli K-12
|
3.2585+/-0.17316
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
|
by FISH
|
PMID:20671182
|-
|
mRNA
|
Ecoli K-12
|
1.078871201
|
Molecules/cell
|
*Medium: 
*Temperature (°C): 
*Doubling time (min): Growth Rate(min):  *
*Growth phase: other:  *
|
|
by RNA_Seq
|
PMID:20671182
|-
|
Protein
|
''E. coli'' K-12 [http://ecoliwiki.net/colipedia/index.php/Category:Strain:EMG2 EMG2]
|
1210
|
molecules/cell
|
*Medium: MOPS glucose minimal
*Temperature (°C): 37
*Doubling time (min):
*Growth phase: Exponential
*OD: OD600 = 0.2 to 0.25 
*other: aerated
|
Quantitative protein sequencing
|
Spot ID: 1\13
|
PMID: 9298646
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
30603
|
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
|
8213
|
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
|
18320
|
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.42199.C49c01dc780cd6-->
===Notes===
==Transcription and Transcriptional Regulation==
==Transcription and Transcriptional Regulation==
{{BacktoTop}}
<protect>
<protect>
{|{{Prettytable}}
{|{{Prettytable}}
|-
|-
|<!--box uid=421aa90e079fa326b6494f812ad13e79..I46a05b6b483ba-->
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|- {{table heading style}}
|- {{table heading style}}
!Transcription unit(s)
!|Transcription unit(s)
|-
|-  
|
|
[[:Category:Txn_unit:atpBEFHAGDC|atpBEFHAGDC]]  
[[:Category:Txn_unit:atpBEFHAGDC|atpBEFHAGDC]]  
|-class='sortbottom'
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|
[[:Category:Txn_unit:atpIBEFHAGDC|atpIBEFHAGDC]]
 
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<!--box uid=421aa90e079fa326b6494f812ad13e79..I46a05b6b483ba-->||{{RegulonDBfig|ECK120000097.jpg|ATPD}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.42199.S46ab8198da566-->||{{RegulonDBfig|ECK120000097.jpg|ECK120000097}}
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{{expression_transcription_help}}
 
<!--Transcription_notes--></protect>
<!--Transcription_notes--></protect>
===Notes===
===Notes===
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==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
<protect>{{GBrowseFigureByCoord|3915383|3915413|ecoli|MG1655|GenesNew+DNA}}
{{BacktoTop}}
{{Expression_translation_help}}
<protect><gbrowseImage>
name=NC_000913:3915378..3915418
source=MG1655
flip=1
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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!|Allele Name!!Mutation!!Phenotype!!Reference
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===Expression Studies===
 
<!--box uid=421aa90e079fa326b6494f812ad13e79..L46a05b6bddcfa-->
<big>'''Expression Studies'''</big>
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. *** -->
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!Type!!Reference!!Notes
!|Type!!Reference!!Notes
|-class='sortbottom'
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|
microarray
|
[[geoprofiles:b3732|GEO Profiles:b3732]] ([[Gene_Expression_Omnibus_%28GEO%29|EcoliWiki Page]])
|
NCBI GEO profiles for ''atpD''
|-
|
microarray
|
[http://genexpdb.ou.edu/index.php?query=b3732 GenExpDB:b3732] ([[EcoliGenExpDB|EcoliWiki Page]])
|
Summary of data for atpD from multiple microarray studies 
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.42199.Z46ab819a21ff1&page=42199&pagename={{FULLPAGENAMEE}}&type=&template=Expression_studies_table edit table]</span> || ||
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===Expression Resources===
 
<!--box uid=421aa90e079fa326b6494f812ad13e79..K46a05b6c123a6-->
<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 atpD Expression==
==Accessions Related to ''atpD'' Expression==
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{{BacktoTop}}
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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=EG10101 EcoCyc:EG10101] 
EcoCyc:EG10101
|
|
''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=EB0099 EchoBASE:EB0099] 
EchoBASE:EB0099
|
|
''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=b3732 EcoliGenExpDB:b3732]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3732 EcoliGenExpDB:b3732]
|
|
   
   
|-
|-
|
[[EcoGene]]
|
EcoGene:EG10101
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120000097
|
''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=EG10101 EcoGene:EG10101] 
ASAP:ABE-0012208
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-class='sortbottom'
 
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{{Expression_accessions_table_help}}
 
<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:atpBEFHAGDC]]
[[Category:Txn_unit:atpIBEFHAGDC]]

Latest revision as of 19:51, 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

3.11E+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

685.856+/-3.117

Molecules/cell

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

Single Molecule Fluorescence

PMID:20671182[2]

mRNA

Ecoli K-12

3.2585+/-0.17316

Molecules/cell

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

by FISH

PMID:20671182[2]

mRNA

Ecoli K-12

1.078871201

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 EMG2

1210

molecules/cell

  • Medium: MOPS glucose minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • Growth phase: Exponential
  • OD: OD600 = 0.2 to 0.25
  • other: aerated

Quantitative protein sequencing

Spot ID: 1\13

PMID:9298646[3]

Protein

E. coli K-12 MG1655

30603

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[4]

Protein

E. coli K-12 MG1655

8213

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[4]

Protein

E. coli K-12 MG1655

18320

molecules/cell/generation

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

Ribosome Profiling

PMID:24766808[4]

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)

atpBEFHAGDC

atpIBEFHAGDC

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

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<gbrowseImage> name=NC_000913:3915378..3915418 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:b3732 (EcoliWiki Page)

NCBI GEO profiles for atpD

microarray

GenExpDB:b3732 (EcoliWiki Page)

Summary of data for atpD 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 atpD Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG10101

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0099

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3732

EcoGene

EcoGene:EG10101

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000097

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012208

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

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  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 Taniguchi, Y et al. (2010) Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells. Science 329 533-8 PubMed
  3. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  4. ↑ 4.0 4.1 4.2 Li, GW et al. (2014) Quantifying absolute protein synthesis rates reveals principles underlying allocation of cellular resources. Cell 157 624-35 PubMed

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