yfdR:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
imported>WikiEntryBot
Automated import of articles
touch
 
(36 intermediate revisions by 2 users not shown)
Line 14: Line 14:
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
Line 27: Line 29:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|   id="Q46a9dc38b3c09"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''yfdR''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''yfdR''
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2355, b2361, JW2358''<ref name='LIB:Riley_2006'/>, JW2358''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.Q46a9dc38b3c09&page=15285&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK2355, b2361, JW2358''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.Q46a9dc38b3c09&page=15285&pagename={{FULLPAGENAMEE}} edit table]
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.Q46a9dc38b3c09-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.Q46a9dc38b3c09-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
Line 59: Line 63:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' {{Prettytable}} id='139051'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9dc393ceca"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
|
|
MG1655
MG1655
Line 72: Line 76:
53.3 minutes, 53.3 minutes&nbsp;
53.3 minutes, 53.3 minutes&nbsp;
|
|
MG1655: 2473006..2473542<br />{{GBrowseFigureByCoord|2472006|2474542|ecoli|MG1655}}
MG1655: 2473006..2473542<br /><gbrowseImage>
name=NC_000913:2473006..2473542
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7230 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7230 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2472006..2474542 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2472006|2474542|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2473006..2473542&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2473006|2473542|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7230 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7230 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 2358811..2359347<br /><gbrowseImage>
name=NC_012759:2358811..2359347
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2358811|2359347|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2358811|2359347|FASTA Dump}}
|-  
|
|
W3110
W3110
Line 86: Line 111:
&nbsp;
&nbsp;
|
|
W3110: 2480430..2480966<br />{{GBrowseFigureByCoord|2479430|2481966|ecoli_W3110|W3110}}
W3110: 2480430..2480966<br /><gbrowseImage>
name=NC_007779:2480430..2480966
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2479430..2481966 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2479430|2481966|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2480430..2480966&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2480430|2480966|FASTA Dump}}
|-class='sortbottom'
|-
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.O46a9dc393ceca&page=15285&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|
[[DH10B]]
|
 
|
DH10B: 2564771..2565307<br /><gbrowseImage>
name=NC_010473:2564771..2565307
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2563699|2566379|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2563699|2566379|FASTA Dump}}
 
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.O46a9dc393ceca&page=15285&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.O46a9dc393ceca-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.O46a9dc393ceca-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
Line 105: Line 152:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='139052'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9dc39e909e"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc39e909e&page=15285&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc39e909e&page=15285&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc39e909e-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc39e909e-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 126: Line 174:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' {{Prettytable}} id='139053'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a9dc3a3ad79"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|-  
|
|
&Delta;yfdR (Keio:JW2358)
&Delta;yfdR (Keio:JW2358)
Line 145: Line 193:


|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108165 CGSC9884]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;yfdR769::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[[cgscmutation:104722|CGSC:104722]]
|
|
   
   
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.R46a9dc3a3ad79&page=15285&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.R46a9dc3a3ad79&page=15285&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.R46a9dc3a3ad79-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.R46a9dc3a3ad79-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15285.R4e04c912a720f-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R4e04c912a720f"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.15285.R4e04c912a720f&page=15285&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15285.R4e04c912a720f--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
Line 164: Line 252:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' {{Prettytable}} id='139054'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9dc3ae69fa"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|
JW2358
JW2358
Line 179: Line 267:
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
|
[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
Line 186: Line 274:


Primer 2:CCTGCGCATTTGCGTAACTCCGA  
Primer 2:CCTGCGCATTTGCGTAACTCCGA  
|-
|-
|
[[:Category:Kohara_Phage:3A11|3A11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=411 Genobase]
|
PMID:3038334
|-  
|
|
[[yfbO:Gene|zfb-223::Tn10]]
[[yfbO:Gene|zfb-223::Tn10]]
Line 194: Line 291:
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zej-223::Tn10  
Synonyms:zej-223::Tn10  
|-
|-  
|
|
zfd-1::Tn10
zfd-1::Tn10
Line 205: Line 301:
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
CAG18467 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40075 CGSC7408]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 51% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 51% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zfb-1::Tn10


Synonyms:zfb-1::Tn10
|- class="tableEdit_footer"
|-class='sortbottom'
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.T46a9dc3ae69fa&page=15285&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.T46a9dc3ae69fa&page=15285&pagename={{FULLPAGENAMEE}} edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.T46a9dc3ae69fa-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.T46a9dc3ae69fa-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 222: Line 318:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' {{Prettytable}} id='139055'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B46a9dc3b87b9f"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G7230
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7230 EcoCyc:G7230] 
EcoGene:EG14140
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3892 EchoBASE:EB3892] 
RegulonDB:ECK120003805
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2361 EcoliGenExpDB:b2361]
[http://www.ncbi.nlm.nih.gov/gene?term=946834 GeneID:946834]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3202 ECOL199310CYC:C3202] 
EchoBASE:EB3892
|
|
''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=EG14140 EcoGene:EG14140] 
ASAP:ABE-0007791
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc3b87b9f&page=15285&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc3b87b9f&page=15285&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc3b87b9f-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.B46a9dc3b87b9f-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 278: Line 382:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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='98477'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a6f94b5cbe0"  class=" tableEdit Links_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
|-class='sortbottom'
 
|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.T46a6f94b5cbe0&page=15285&pagename={{FULLPAGENAMEE}} edit table] || ||
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15285.T46a6f94b5cbe0&page=15285&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.T46a6f94b5cbe0-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.15285.T46a6f94b5cbe0-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
Line 295: Line 400:
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
Line 303: Line 407:
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yfd genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 19 September 2013

{{#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 Sequence Features Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

[back to top]


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

Standard name

yfdR

Mnemonic

Systematic nomenclature

Synonyms

ECK2355, b2361, JW2358[1], JW2358

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

Strain Map location Genome coordinates Genome browsers Sequence links

MG1655

53.3 minutes, 53.3 minutes 

MG1655: 2473006..2473542
<gbrowseImage> name=NC_000913:2473006..2473542 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2358811..2359347
<gbrowseImage> name=NC_012759:2358811..2359347 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2480430..2480966
<gbrowseImage> name=NC_007779:2480430..2480966 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2564771..2565307
<gbrowseImage> name=NC_010473:2564771..2565307 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

Feature Type Strain Genomic Location Evidence Reference Notes
edit table


Notes

Alleles and Phenotypes

[back to top]


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

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

ΔyfdR (Keio:JW2358)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9884[3]

ΔyfdR769::kan

PMID:16738554[2]

CGSC:104722


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


Notes

Genetic Resources

[back to top]


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

Resource Resource Type Source Notes/Reference

JW2358

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCATTTATTAAAACTTTTTC

Primer 2:CCTGCGCATTTGCGTAACTCCGA

3A11

Kohara Phage

Genobase

PMID:3038334[5]

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[3]

est. P1 cotransduction: % [6]
Synonyms:zej-223::Tn10

zfd-1::Tn10

Linked marker

CAG18467 = CGSC7408[3]

est. P1 cotransduction: 51% [6]
Synonyms:zfb-1::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


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

Database Accession Notes

EcoCyc

EcoCyc:G7230

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14140

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003805

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946834

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3892

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007791

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

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. ↑ 2.0 2.1 Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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
  5. ↑ Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  6. ↑ 6.0 6.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

Categories

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=yfdR:Gene&oldid=1478815"