yaaH:Expression: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Fixing references section.
Edited by EditTablesByTemplate.php maintenance script
 
(9 intermediate revisions by the same user not shown)
Line 36: Line 36:
*  
*  
****************************************************************************************** -->{{Help Cellular levels}}
****************************************************************************************** -->{{Help Cellular levels}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A49c03a0b14f79"  class=" tableEdit MoleculesPerCellTable"   
|- align='left' bgcolor='#CCCCFF'
|- 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 MG1655
|
1461
|
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
|
38
|
molecules/cell/generation
|
*Medium: MOPS Minimal 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|


|-class='sortbottom'
|
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.32512.A49c03a0b14f79&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=MoleculesPerCellTable edit table] || || || || || || || || || ||
PMID: 24766808
|-
|
Protein
|
''E. coli'' K-12 MG1655
|
63<sup>a</sup>
 
|
molecules/cell/generation
|
*Medium: MOPS Complete without Methionine 
* Temperature (°C):  37
*Doubling time (min):
* *Growth phase: 
*OD:
*other:
|
Ribosome Profiling
|
Low confidence in the sequencing data set.
|
PMID: 24766808
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.32512.A49c03a0b14f79&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=MoleculesPerCellTable edit table]</span> || || || || || || ||
|}
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.32512.A49c03a0b14f79-->
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.32512.A49c03a0b14f79-->
Line 59: Line 126:
*  
*  
****************************************************************************************** -->{{expression_transcription_help}}
****************************************************************************************** -->{{expression_transcription_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46ab3584205ef"  class=" tableEdit Expression_operons_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Transcription unit(s)
!|Transcription unit(s)
Line 66: Line 133:
[[:Category:Txn_unit:yaaH|yaaH]]  
[[:Category:Txn_unit:yaaH|yaaH]]  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.F46ab3584205ef&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_operons_table edit table]
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.F46ab3584205ef&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_operons_table edit table]</span>
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.F46ab3584205ef-->||{{RegulonDBfig|ECK120001468.jpg|YAAH}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.F46ab3584205ef-->||{{RegulonDBfig|ECK120001468.jpg|ECK120001468}}
|}
|}


Line 78: Line 145:
==Translation and Regulation of Translation==
==Translation and Regulation of Translation==
{{BacktoTop}}
{{BacktoTop}}
<protect>{{GBrowseFigureByCoord|10474|10514|ecoli|MG1655|Genes_unlabeled+DNA_unlabeled+flip|400|{{Nterm_closeup}} }}
<protect><gbrowseImage>
name=NC_000913:10474..10514
source=MG1655
flip=1
type=Gene+DNA_+Protein
preset=Nterminus
</gbrowseImage>
{{Nterm_closeup}}
 
<!--Translation_notes--></protect>
<!--Translation_notes--></protect>
===Notes===
===Notes===
Line 100: Line 175:
*  
*  
****************************************************************************************** -->{{Expression_allele_table_help}}
****************************************************************************************** -->{{Expression_allele_table_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46ab3584e191b"  class=" tableEdit Expression_allele_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Allele Name!!Mutation!!Phenotype!!Reference
!|Allele Name!!Mutation!!Phenotype!!Reference


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.T46ab3584e191b&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_allele_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.T46ab3584e191b&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_allele_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.T46ab3584e191b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.T46ab3584e191b-->
Line 118: Line 193:
*  
*  
****************************************************************************************** -->{{Expression_studies_table_help}}
****************************************************************************************** -->{{Expression_studies_table_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46ab358554c07"  class=" tableEdit Expression_studies_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Type!!Reference!!Notes
!|Type!!Reference!!Notes
|-  
|-  
|
|
microarray  
microarray
|
|
[http://genexpdb.ou.edu/index.php?query=b0010 GenExpDB:b0010] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://genexpdb.ou.edu/index.php?query=b0010 GenExpDB:b0010] ([[EcoliGenExpDB|EcoliWiki Page]])  
Line 136: Line 211:
NCBI GEO profiles for ''yaaH''  
NCBI GEO profiles for ''yaaH''  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.G46ab358554c07&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_studies_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.G46ab358554c07&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_studies_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.G46ab358554c07-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.G46ab358554c07-->
Line 150: Line 225:
*  
*  
****************************************************************************************** -->{{Expression_resource_table_help}}
****************************************************************************************** -->{{Expression_resource_table_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46ab3585bcd30"  class=" tableEdit Expression_resource_table"   
|- {{table heading style}}
|- {{table heading style}}
!|Resource Name!!Resource Type!!Description!!Source!!Notes
!|Resource Name!!Resource Type!!Description!!Source!!Notes
Line 165: Line 240:
GFP fusion described in Zaslaver, <i>et al.</i><br />Plate:109-AZ01; Well:E3<ref name="PMID: 16862137" />  
GFP fusion described in Zaslaver, <i>et al.</i><br />Plate:109-AZ01; Well:E3<ref name="PMID: 16862137" />  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.Z46ab3585bcd30&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_resource_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.Z46ab3585bcd30&page=32512&pagename={{FULLPAGENAMEE}}&type=&template=Expression_resource_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.Z46ab3585bcd30-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.Z46ab3585bcd30-->
Line 183: Line 258:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46ab358637219"  class=" tableEdit Gene_accessions_table"   
|- {{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=EG11512 EcoCyc:EG11512]
EcoCyc:EG11512
|
|
''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=EB1474 EchoBASE:EB1474]
EchoBASE:EB1474
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
Line 209: Line 284:
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EcoGene]]
|
EcoGene:EG11512
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120001468
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11512 EcoGene:EG11512]
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
|
|
[[ASAP]]
|
ASAP:ABE-0000032
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.E46ab358637219&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.E46ab358637219&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.E46ab358637219-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.E46ab358637219-->
Line 233: Line 322:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a7a3abe7b51"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.B46a7a3abe7b51&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.32512.B46a7a3abe7b51&page=32512&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.B46a7a3abe7b51-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.32512.B46a7a3abe7b51-->

Latest revision as of 18:56, 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

1461

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

38

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

63a

molecules/cell/generation

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

Ribosome Profiling

Low confidence in the sequencing data set.

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)

yaaH

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_000913:10474..10514 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

GenExpDB:b0010 (EcoliWiki Page)

Summary of data for yaaH from multiple microarray studies

microarray

GEO Profiles:b0010 (EcoliWiki Page)

NCBI GEO profiles for yaaH

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 (10405..10754) fused to gfpmut2.

OpenBioSystems

GFP fusion described in Zaslaver, et al.
Plate:109-AZ01; Well:E3[2]

edit table

<protect>

Notes

Accessions Related to yaaH Expression

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:EG11512

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1474

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0010

EcoGene

EcoGene:EG11512

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001468

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000032

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



References

[back to top]


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. ↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=yaaH:Expression&oldid=1499392"