EcoliWiki - User contributions [en]

Talk:dinB:Gene

2007-08-08T20:06:26Z

Smrlab: Add Phenotype type

{{Gene talk placeholder}}

== Add Phenotype type ==

decreased mutagenesis, recombination defective (Rec-)

EcoliWiki:Wishlist

2007-08-08T20:04:07Z

Smrlab: /* What we would like to see? */

==Wishlist==
The EcoliWiki team strives to make the Wiki better. To that end, we are asking for your opinion. If there is a feature not currently available in EcoliWiki that you would like to see, describe it here.

===What's up and coming for EcoliWiki v2===
*Searching for information present in the tables specifically
*If I search for multiple genes in EcoliWiki, it would be nice for the output to be given in some delimited form.

===What we would like to see?===
*Search and type greek and non-English characters or some toolbar for it (lambda vs. the symbol, delta, sigma, etc.)
*Video clip upload
*Search for phenotype and output is a list of genes
*References- DOI's and Pubmed Central IDs (for things w/o PMIDs)
*A "Go To" alphabet to organize the category pages
* RNAs in W3110
** links to RFAM
** pulldown menus for RNAs in Gbrowse
*synthetic lethal database[[User:Smrlab|Smrlab]]
*interactome data base[[User:Smrlab|Smrlab]]

EcoliWiki:Wishlist

2007-08-08T20:03:24Z

Smrlab: /* What we would like to see? */

==Wishlist==
The EcoliWiki team strives to make the Wiki better. To that end, we are asking for your opinion. If there is a feature not currently available in EcoliWiki that you would like to see, describe it here.

===What's up and coming for EcoliWiki v2===
*Searching for information present in the tables specifically
*If I search for multiple genes in EcoliWiki, it would be nice for the output to be given in some delimited form.

===What we would like to see?===
*Search and type greek and non-English characters or some toolbar for it (lambda vs. the symbol, delta, sigma, etc.)
*Video clip upload
*Search for phenotype and output is a list of genes
*References- DOI's and Pubmed Central IDs (for things w/o PMIDs)
*A "Go To" alphabet to organize the category pages
* RNAs in W3110
** links to RFAM
** pulldown menus for RNAs in Gbrowse
synthetic lethal database[[User:Smrlab|Smrlab]]
interactome data base[[User:Smrlab|Smrlab]]

dinB:Gene

2007-08-08T19:52:56Z

Smrlab: edited by Smrlab via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|dinB}}{{Tab On|Gene|dinB}}{{Tab|Gene Product(s)|dinB}}{{Tab|Expression|dinB}}{{Tab|Evolution|dinB}}{{Tab|On One Page|dinB}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''dinB''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.B46a9ab5b1546c&page=11041&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='126321'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
5.41 minutes 
|
MG1655: 250898..251953 {{GBrowseFigureByCoord|249898|252953|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6115 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:249898..252953 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:250898..251953&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G6115 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 250898..251953 {{GBrowseFigureByCoord|249898|252953|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:249898..252953 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:250898..251953&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.O46a9ab5b8e4d7&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126322'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.M46a9ab5c383cc&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126323'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔdinB (Keio:JW0221)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.S46a9ab5c79313&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126324'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW0221
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCCGTAAAATCATTCATGTGGA

Primer 2:CCTAATCCCAGCACCAGTTGTCT
|-
|
[[yafC:Gene|yafC502::Tn10]]
|
Linked marker
|
CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zae-502::Tn10
|-
|
[[proA:Gene|proA81::Tn10]]
|
Linked marker
|
CAG18447 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38993 CGSC7330]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.N46a9ab5d22bd7&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126325'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6115 EcoCyc:G6115]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2935 EchoBASE:EB2935]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C0379 ECOL199310CYC:C0379]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG13141 EcoGene:EG13141]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=DINP ECOO157CYC:DINP]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.V46a9ab5dacd15&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='96357'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.A46a678908ee59&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

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

dinB:Gene

2007-08-08T19:52:30Z

Smrlab: edited by Smrlab via TableEdit

{{#css:Suppresslinks.css}}<css>{{:Suppresslinks.css}}</css>
<noinclude>{{TabsTop}}
{{Tab|Quickview|dinB}}{{Tab On|Gene|dinB}}{{Tab|Gene Product(s)|dinB}}{{Tab|Expression|dinB}}{{Tab|Evolution|dinB}}{{Tab|On One Page|dinB}}{{TabsBottom}}
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Resources |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Links |Links]]
|{{Sub}}[[#References |References]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
</noinclude><protect>
==Nomenclature==
{{BacktoTop}}


{|{{Prettytable}}
|-
!{{table_heading_style}} |Standard name
|
''dinB''
|-
!{{table_heading_style}} |Mnemonic
|

|-
!{{table_heading_style}} |Synonyms
|
''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.B46a9ab5b1546c&page=11041&pagename={{FULLPAGENAMEE}} edit table]
|}

{{Gene_nomenclature_help}}
</protect>
===Notes===

==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>


{|class = 'sortable' {{Prettytable}} id='126321'
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|
MG1655
|
5.41 minutes 
|
MG1655: 250898..251953 {{GBrowseFigureByCoord|249898|252953|ecoli|MG1655}}
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6115 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:249898..252953 GBrowse(MG1655)]

|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:250898..251953&plugin_action=Go FASTA Dump]
*[http://biocyc.org/ECOLI/sequence?object=G6115 EcoCyc Sequence Dump]
|-
|
W3110
|
 
|
W3110: 250898..251953 {{GBrowseFigureByCoord|249898|252953|ecoli_W3110|W3110}}
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:249898..252953 GBrowse(W3110)]
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:250898..251953&plugin_action=Go FASTA Dump]
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.O46a9ab5b8e4d7&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|}

{{Gene_location_help}}
</protect>
===Notes===

==Sequence Features==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126322'
|- {{table_heading_style}}
!Feature type!!Location!!Description
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.M46a9ab5c383cc&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_sequence_features_help}}
<protect></protect>
====Notes====

==Alleles and Phenotypes==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126323'
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
ΔdinB (Keio:JW0221)
|
deletion
|
deletion
|

|

|
[[PMID:16738554]]<ref name=PMID:16738554/>
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|

|-
|
dinB1[[User:Smrlab|Smrlab]]
|
dinB[[User:Smrlab|Smrlab]] 14:52, 8 August 2007 (CDT)
|

|

|

|

|

|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.S46a9ab5c79313&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|}

{{Gene_alleles_help}}
<protect></protect>
===Notes===

==Genetic Resources==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126324'
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
|-
|
JW0221
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
[[PMID:16769691]]<ref name=PMID:16769691/>

Status:Clone OK

Primer 1:GCCCGTAAAATCATTCATGTGGA

Primer 2:CCTAATCCCAGCACCAGTTGTCT
|-
|
[[yafC:Gene|yafC502::Tn10]]
|
Linked marker
|
CAG18436 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38989 CGSC7328]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 50% <ref name='LIB:Nichols_linked_Tn'/>

Synonyms:zae-502::Tn10
|-
|
[[proA:Gene|proA81::Tn10]]
|
Linked marker
|
CAG18447 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38993 CGSC7330]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 74% <ref name='LIB:Nichols_linked_Tn'/>
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.N46a9ab5d22bd7&page=11041&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}

{{Gene_resources_help}}
<protect></protect>
===Notes===

==Accessions in Other Databases==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='126325'
|- {{table_heading_style}}
!Database!!Accession!!Notes
|-
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6115 EcoCyc:G6115]
|

|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2935 EchoBASE:EB2935]
|

|-
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0231 EcoliGenExpDB:b0231]
|

|-
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C0379 ECOL199310CYC:C0379]
|

|-
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
|
[http://ecogene.org/geneinfo.php?eg_id=EG13141 EcoGene:EG13141]
|

|-
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=DINP ECOO157CYC:DINP]
|

|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.V46a9ab5dacd15&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Gene_accessions_help}}
<protect></protect>
===Notes===

==Links==
{{BacktoTop}}


{|class = 'sortable' {{Prettytable}} id='96357'
|- {{table_heading_style}}
!Name!!URL!!Comments
|-class='sortbottom'
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11041.A46a678908ee59&page=11041&pagename={{FULLPAGENAMEE}} edit table] || ||
|}

{{Links_help}}

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

SMR10

2007-08-08T19:44:32Z

Smrlab: New page: ==Alternate Names {{HelpIcon|Help:Strains}}== ==Chromosomal Genotype {{HelpIcon|Help:Strains}}== ==Plasmids {{HelpIcon|Help:Strains}}== ==Phage {{HelpIcon|Help:Strains}}== ==Phenotypes...

==Alternate Names {{HelpIcon|Help:Strains}}==

==Chromosomal Genotype {{HelpIcon|Help:Strains}}==

==Plasmids {{HelpIcon|Help:Strains}}==

==Phage {{HelpIcon|Help:Strains}}==

==Phenotypes {{HelpIcon|Help:Strains}}==

==Construction {{HelpIcon|Help:Strains}}==

==Notes==

==References==
{{RefHelp}}
<references/>

__NOTOC__
[[Category:Strains]]