hda:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
imported>WikiEntryBot
Automated import of articles
imported>WikiEntryBot
Automated import of articles
Line 1: Line 1:
<!--PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE, YOU'RE PROBABLY IN THE WRONG PLACE-->
<!--
***************************************************************************************************************************************************
*
*              PLEASE EDIT FROM THE SECTION OR TABLE EDIT LINKS...IF YOU SEE THIS MESSAGE,
*                            YOU'RE PROBABLY IN THE WRONG PLACE
*
*
***************************************************************************************************************************************************
-->{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|hda}}{{Tab On|Gene|hda}}{{Tab|Gene Product(s)|hda}}{{Tab|Expression|hda}}{{Tab|Evolution|hda}}{{Tab|On One Page|hda}}{{TabsBottom}}
{{Tab|Quickview|hda}}{{Tab On|Gene|hda}}{{Tab|Gene Product(s)|hda}}{{Tab|Expression|hda}}{{Tab|Evolution|hda}}{{Tab|On One Page|hda}}{{TabsBottom}}
Line 13: Line 21:
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
<!--box uid=421aa90e079fa326b6494f812ad13e79..X469faca411865-->
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Q46a9df5cb005b-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|{{Prettytable}}
{|{{Prettytable}}
Line 31: Line 41:
''ECK2492, b2496, JW5397, idaB, yfgE, dp''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK2492, b2496, JW5397, idaB, yfgE, dp''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..X469faca411865&page=&pagename={{FULLPAGENAMEE}} edit table]
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.Q46a9df5cb005b&page=15559&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..X469faca411865-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Q46a9df5cb005b-->
{{Gene_nomenclature_help}}
{{Gene_nomenclature_help}}
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
Line 40: Line 50:


==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469faca458ed0-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.P46a9df5d3a7ab-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='19468'  
{|class = 'sortable' {{Prettytable}} id='139873'  
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
Line 72: Line 83:
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2616731..2617477&plugin_action=Go FASTA Dump]  
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2616731..2617477&plugin_action=Go FASTA Dump]  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..V469faca458ed0&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.P46a9df5d3a7ab&page=15559&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469faca458ed0-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.P46a9df5d3a7ab-->
{{Gene_location_help}}
{{Gene_location_help}}
<!--Location_notes--></protect>
<!--Location_notes--></protect>
Line 81: Line 92:


==Sequence Features==
==Sequence Features==
<!--box uid=421aa90e079fa326b6494f812ad13e79..H469faca474649-->
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Z46a9df5de776a-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='19469'  
{|class = 'sortable' {{Prettytable}} id='139874'  
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!Feature type!!Location!!Description
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..H469faca474649&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.Z46a9df5de776a&page=15559&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..H469faca474649-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Z46a9df5de776a-->
{{Gene_sequence_features_help}}
{{Gene_sequence_features_help}}
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
Line 96: Line 108:


==Alleles and Phenotypes==
==Alleles and Phenotypes==
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469faca47f525-->
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.O46a9df5e39304-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='19470'  
{|class = 'sortable' {{Prettytable}} id='139875'  
|- {{table_heading_style}}
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!CGSC Mutation ID #
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
|-
|-
|
|
&nbsp;
&Delta;hda (Keio:JW5397)
|
|
&nbsp;
deletion
|
|
&nbsp;
deletion
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
[[PMID:1673855]]<ref name=PMID:1673855/>
|
|
&nbsp;
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..V469faca47f525&page=&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.O46a9df5e39304&page=15559&pagename={{FULLPAGENAMEE}} edit table] || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..V469faca47f525-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.O46a9df5e39304-->
{{Gene_alleles_help}}
{{Gene_alleles_help}}
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
Line 126: Line 139:


==Genetic Resources==
==Genetic Resources==
<!--box uid=421aa90e079fa326b6494f812ad13e79..B469faca48a40f-->
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.N46a9df5ee8c22-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='19471'  
{|class = 'sortable' {{Prettytable}} id='139876'  
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!Resource!!Resource Type!!Source!!Notes/Reference
Line 147: Line 161:
Primer 2:CCtAACTTCAGAATTTCTTTCAC  
Primer 2:CCtAACTTCAGAATTTCTTTCAC  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..B469faca48a40f&page=&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.N46a9df5ee8c22&page=15559&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..B469faca48a40f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.N46a9df5ee8c22-->
{{Gene_resources_help}}
{{Gene_resources_help}}
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
Line 156: Line 170:


==Accessions in Other Databases==
==Accessions in Other Databases==
<!--box uid=421aa90e079fa326b6494f812ad13e79..R469faca4952b3-->
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.V46a9df5f8ab88-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='19472'  
{|class = 'sortable' {{Prettytable}} id='139877'  
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!Database!!Accession!!Notes
Line 204: Line 219:
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..R469faca4952b3&page=&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.V46a9df5f8ab88&page=15559&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79..R469faca4952b3-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.V46a9df5f8ab88-->
{{Gene_accessions_help}}
{{Gene_accessions_help}}
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
Line 213: Line 228:


==Links==
==Links==
{{BacktoTop}}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de-->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
<!--*** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. ***  -->
{|class = 'sortable' {{Prettytable}} id='98614'  
{|class = 'sortable' {{Prettytable}} id='98614'  
|-
|- {{table_heading_style}}
!
!Name!!URL!!Comments
|-
|
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de&page=15559&pagename={{FULLPAGENAMEE}} edit table]
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de&page=15559&pagename={{FULLPAGENAMEE}} edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15559.Y46a6fc36112de-->
{{Links_help}}


<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references/>
__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
</protect></noinclude>

Revision as of 12:04, 27 July 2007

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Alleles and Phenotypes Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


Standard name

hda

Mnemonic
Synonyms

ECK2492, b2496, JW5397, idaB, yfgE, dp[1][2]

edit table

See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Notes

Location(s) and DNA Sequence

[back to top]


Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

56.39 minutes 

MG1655: 2616843..2616097
gbrowse_img.php?coord=2615097..2617843&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 2617477..2616731
gbrowse_img.php?coord=2615731..2618477&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit table

See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

[back to top]


Feature type Location Description
edit table

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

[back to top]


Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability

Δhda (Keio:JW5397)

deletion

deletion

PMID:1673855[3]

Shigen

edit table

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

[back to top]


Resource Resource Type Source Notes/Reference

JW5397

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGTAAACTTCTCGCGATTTTG

Primer 2:CCtAACTTCAGAATTTCTTTCAC

edit table

See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

[back to top]


Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G7313

EchoBASE (EcoliWiki Page)

EchoBASE:EB3953

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2496

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3013

EcoGene (EcoliWiki Page)

EcoGene:EG14201

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z3759

edit table

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

Notes

Links

[back to top]


Name URL Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References

[back to top]


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

  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Schultz, RM (1991) The role of metalloproteinases in tumor cell metastasis. Cancer Treat. Res. 54 119-33 PubMed
  4. ↑ Kitagawa, M et al. (2005) Complete set of ORF clones of Escherichia coli ASKA library (a complete set of E. coli K-12 ORF archive): unique resources for biological research. DNA Res. 12 291-9 PubMed


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=hda:Gene&oldid=161463"