queD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|sscR}}{{Tab On|Gene|sscR}}{{Tab|Gene Product(s)|sscR}}{{Tab|Expression|sscR}}{{Tab|Evolution|sscR}}{{Tab|On One Page|sscR}}{{TabsBottom}}
{{Tab|Quickview|queD}}{{Tab On|Gene|queD}}{{Tab|Gene Product(s)|queD}}{{Tab|Expression|queD}}{{Tab|Evolution|queD}}{{Tab|On One Page|queD}}{{TabsBottom}}
{|
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|{{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]]
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==Nomenclature==
==Nomenclature==
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{|  id="T46a9e5b346b4d"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''sscR''  
''queD''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Queosine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ygcM, ECK2760, b2765, JW2735, ptpS'', sscR<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>, sscR''


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!{{table_heading_style}} |Synonyms
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''ygcM, ECK2760, b2765, JW2735, ptpS''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
|-
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e5b3c5869"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-
|-  
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MG1655
MG1655
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62.29 minutes&nbsp;
62.29 minutes&nbsp;
|
|
MG1655: 2890236..2890601<br />{{GBrowseFigureByCoord|2889236|2891601|ecoli|MG1655}}
MG1655: 2890236..2890601<br /><gbrowseImage>
name=NC_000913:2890236..2890601
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7431 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7431 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2889236..2891601 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|2889236|2891601|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2890236..2890601&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|2890236|2890601|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7431 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7431 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 2776048..2776413<br /><gbrowseImage>
name=NC_012759:2776048..2776413
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|2776048|NC_2776413|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|2776048|NC_2776413|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2890870..2891235<br />{{GBrowseFigureByCoord|2889870|2892235|ecoli_W3110|W3110}}  
W3110: 2890870..2891235<br /><gbrowseImage>
name=NC_007779:2890870..2891235
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|2889870|2892235|GBrowse(W3110)}}
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|2890870|2891235|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 2982778..2983143<br /><gbrowseImage>
name=NC_010473:2982778..2983143
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2889870..2892235 GBrowse(W3110)]
{{GBrowseLink|ecoli_DH10B|NC_010473|2982048|2983873|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2890870..2891235&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|2982048|2983873|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{|  id="Q46a9e5b4807f9"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| {{Prettytable}} id="W46a9e5b4c725c"  class=" tableEdit Gene_allele_table dataTable" 
|- {{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!!Comments
|-
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''&#916;sscR767::kan''
|
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
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&nbsp;
 
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&nbsp;
PMID:16738554
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&nbsp;
[[cgscmutation:106348|CGSC:106348]]
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&nbsp;
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16095.X4e04c1f5b1831-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X4e04c1f5b1831"  class=" tableEdit Genetic_interaction_table dataTable" 
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|- class="tableEdit_footer"
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{|  id="W46a9e5b5828ff"  class=" tableEdit Gene_resource_table" 
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!|Resource!!Resource Type!!Source!!Notes/Reference
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[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:
Status:
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Primer 2:  
Primer 2:  
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[[:Category:Kohara_Phage:9A10|9A10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=453 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1B3|1B3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=454 Genobase]
|
PMID:3038334
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7431 EcoCyc:G7431]
[http://chase.ou.edu/macro/searchlink.php?bnum=b2765 EcoliGenExpDB:b2765]
|
|
   
   
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2921 EchoBASE:EB2921]
[http://BioCyc.org/ECOL199310/new-image?object=C3324 ECOL199310CYC:C3324]
|
|
   
   
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2765 EcoliGenExpDB:b2765]
[http://BioCyc.org/ECOO157/new-image?object=YGCM ECOO157CYC:YGCM]
|
|
   
   
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3324 ECOL199310CYC:C3324]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7431 ECOCYC:G7431]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13120 EcoGene:EG13120]
[http://www.ncbi.nlm.nih.gov/gene?term=945123 GeneID:945123]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YGCM ECOO157CYC:YGCM] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
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==References==
==References==
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[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ssc genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:que genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 19 September 2013

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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

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

Standard name

queD

Mnemonic

Queosine

Synonyms

ygcM, ECK2760, b2765, JW2735, ptpS, sscR[1][2][3], sscR

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Notes

Location(s) and DNA Sequence

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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

62.29 minutes 

MG1655: 2890236..2890601
<gbrowseImage> name=NC_000913:2890236..2890601 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2776048..2776413
<gbrowseImage> name=NC_012759:2776048..2776413 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2890870..2891235
<gbrowseImage> name=NC_007779:2890870..2891235 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2982778..2983143
<gbrowseImage> name=NC_010473:2982778..2983143 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

ΔsscR767::kan

PMID:16738554[4]

CGSC:106348


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Notes

Genetic Interactions

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

Genetic Resources

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

Resource Resource Type Source Notes/Reference

Plasmid clone

Shigen

PMID:16769691[5]

Status:

Primer 1:

Primer 2:

9A10

Kohara Phage

Genobase

PMID:3038334[6]

1B3

Kohara Phage

Genobase

PMID:3038334[6]

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Notes

Accessions in Other Databases

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

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2765

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3324

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YGCM

EcoCyc (EcoliWiki Page)

ECOCYC:G7431

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945123

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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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 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 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
  5. ↑ 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
  6. ↑ 6.0 6.1 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

Categories

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