pptA:Gene: Difference between revisions

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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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ydcE, ECK1455, b1461, JW1456''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ydcE, ECK1455, b1461, JW1456''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, JW1456''


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{|   id="E46a9c7838d653"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9c7838d653"  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
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33 minutes&nbsp;
33 minutes&nbsp;
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MG1655: 1531076..1531309<br />{{GBrowseFigureByCoord|1531076|1531309|ecoli|MG1655}}
MG1655: 1531076..1531309<br /><gbrowseImage>
name=NC_000913:1531076..1531309
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11761 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11761 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1530076|1532309|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1530076|1532309|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1531076|1531309|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1531076|1531309|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11761 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11761 EcoCyc Sequence Dump]  
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NC_012967: 1507202..1507429<br />{{GBrowseFigureByCoord|1507202|1507429|REL606|NC_012967}}
NC_012967: 1507202..1507429<br /><gbrowseImage>
name=NC_012967:1507202..1507429
source=REL606
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|REL606|NC_012967|1507202|1507429|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|1507202|1507429|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|1507202|1507429|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|1507202|1507429|FASTA Dump}}  
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[[BW2952]]
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NC_012759: 1423135..1423368<br /><gbrowseImage>
name=NC_012759:1423135..1423368
source=BW2952
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|BW2952|NC_012759|1423135|1423368|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|1423135|1423368|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 1534766..1534999<br />{{GBrowseFigureByCoord|1534766|1534999|ecoli_W3110|W3110}}
W3110: 1534766..1534999<br /><gbrowseImage>
name=NC_007779:1534766..1534999
source=W3110
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_W3110|AC_000091|1533766|1535999|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1533766|1535999|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1534766|1534999|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1534766|1534999|FASTA Dump}}  
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DH10B: 1621671..1621904<br />{{GBrowseFigureByCoord|1621671|1621904|ecoli_DH10B|DH10B}}
DH10B: 1621671..1621904<br /><gbrowseImage>
name=NC_010473:1621671..1621904
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
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{{GBrowseLink|ecoli_DH10B|NC_010473|1621205|1622370|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1621205|1622370|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1621205|1622370|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1621205|1622370|FASTA Dump}}  


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{|   id="L46a9c7843c8cd"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9c7843c8cd"  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


|- class="tableEdit_footer"  
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13487.L46a9c7843c8cd&page=13487&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || || || || ||
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{| {{Prettytable}} id="P46a9c7847ee4a"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="P46a9c7847ee4a"  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
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13487.E4e04c16644041-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E4e04c16644041"  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.13487.E4e04c16644041&page=13487&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="W46a9c7852e516"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="W46a9c7852e516"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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{|   id="Y46a9c785bc613"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Y46a9c785bc613"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11761 EcoCyc:EG11761]
EcoCyc:EG11761
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1711 EchoBASE:EB1711]
EcoGene:EG11761
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1461 EcoliGenExpDB:b1461]
RegulonDB:ECK120001697
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG11761 EcoGene:EG11761]
[http://www.ncbi.nlm.nih.gov/gene?term=945731 GeneID:945731]
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Escherichia coli str. K-12 substr. MG1655
|-  
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YDCE ECOO157CYC:YDCE]
EchoBASE:EB1711
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004875&formSubmitReturn=1 ASAP:ABE-0004875]
ASAP:ABE-0004875
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{|   id="R46a6e4f5b3fe2"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R46a6e4f5b3fe2"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ppt genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:ppt genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:29, 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

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

Standard name

pptA

Mnemonic

PhenylPyruvate Tautomerase

Synonyms

ydcE, ECK1455, b1461, JW1456[1][2], JW1456

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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

33 minutes 

MG1655: 1531076..1531309
<gbrowseImage> name=NC_000913:1531076..1531309 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1507202..1507429
<gbrowseImage> name=NC_012967:1507202..1507429 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1423135..1423368
<gbrowseImage> name=NC_012759:1423135..1423368 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1534766..1534999
<gbrowseImage> name=NC_007779:1534766..1534999 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1621671..1621904
<gbrowseImage> name=NC_010473:1621671..1621904 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
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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[3]

Status:

Primer 1:

Primer 2:

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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

EcoCyc

EcoCyc:EG11761

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11761

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001697

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945731

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1711

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004875

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 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

Categories

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