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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|{{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==
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{|  id="Y46a9c78312ba6"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''pptA''  
''pptA''
|-
!align=left {{table_heading_style}} |Mnemonic
||
PhenylPyruvate Tautomerase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ydcE, ECK1455, b1461, JW1456''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>, JW1456''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13487.Y46a9c78312ba6&page=13487&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ydcE, ECK1455, b1461, JW1456''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
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===Notes===
===Notes===
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{| 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
|-
|-  
|
|
MG1655
MG1655
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33 minutes&nbsp;
33 minutes&nbsp;
|
|
MG1655: 1531076..1531309<br />{{GBrowseFigureByCoord|1530076|1532309|ecoli|MG1655}}
MG1655: 1531076..1531309<br /><gbrowseImage>
name=NC_000913:1531076..1531309
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[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]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1530076..1532309 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1530076|1532309|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1531076..1531309&plugin_action=Go 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]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1507202..1507429<br /><gbrowseImage>
name=NC_012967:1507202..1507429
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1507202|1507429|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1507202|1507429|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 1423135..1423368<br /><gbrowseImage>
name=NC_012759:1423135..1423368
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1423135|1423368|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1423135|1423368|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1534766..1534999<br />{{GBrowseFigureByCoord|1533766|1535999|ecoli_W3110|W3110}}
W3110: 1534766..1534999<br /><gbrowseImage>
name=NC_007779:1534766..1534999
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1533766..1535999 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1533766|1535999|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1534766..1534999&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1534766|1534999|FASTA Dump}}
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|
[[DH10B]]
|
 
|
DH10B: 1621671..1621904<br /><gbrowseImage>
name=NC_010473:1621671..1621904
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1621205|1622370|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1621205|1622370|FASTA Dump}}
 
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===Notes===
===Notes===
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{| 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='sortbottom'
 
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====Notes====
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{| 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
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
|
&Delta;pptA (Keio:)
|
deletion
|
deletion
|
 
|


|
|- class="tableEdit_footer"
[[PMID:16738554]]<ref name=PMID:16738554/>
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13487.P46a9c7847ee4a&page=13487&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|-class='sortbottom'
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13487.E4e04c16644041-->
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===Notes===


==Genetic Resources==
==Genetic Resources==
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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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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:EG11761
|
''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=EG11761 EcoCyc:EG11761] 
EcoGene:EG11761
|
|
''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=EB1711 EchoBASE:EB1711] 
RegulonDB:ECK120001697
|
|
''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=b1461 EcoliGenExpDB:b1461]
[http://www.ncbi.nlm.nih.gov/gene?term=945731 GeneID:945731]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11761 EcoGene:EG11761] 
EchoBASE:EB1711
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YDCE ECOO157CYC:YDCE] 
ASAP:ABE-0004875
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
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{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</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: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

[back to top]


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

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

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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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

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