pheL: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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{|{{Prettytable}}
{|   id="H46a9e1d5679c3"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''pheL''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''pheL''
Phenylalanine
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2595, b2598, JW2579, pheAE''<ref name='LIB:Riley_2006'/>, pheAE''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15765.H46a9e1d5679c3&page=15765&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|
''ECK2595, b2598, JW2579, pheAE''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15765.H46a9e1d5679c3&page=15765&pagename={{FULLPAGENAMEE}} edit table]
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='140491'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9e1d5e5735"  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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58.96 minutes&nbsp;
58.96 minutes&nbsp;
|
|
MG1655: 2735621..2735668<br />{{GBrowseFigureByCoord|2734621|2736668|ecoli|MG1655}}
MG1655: 2735621..2735668<br /><gbrowseImage>
name=NC_000913:2735621..2735668
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11271 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11271 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2734621..2736668 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2734621|2736668|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2735621..2735668&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2735621|2735668|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11271 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11271 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2659007..2659054<br /><gbrowseImage>
name=NC_012967:2659007..2659054
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2659007|2659054|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2659007|2659054|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2621433..2621480<br /><gbrowseImage>
name=NC_012759:2621433..2621480
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2621433|2621480|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2621433|2621480|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 2736255..2736302<br />{{GBrowseFigureByCoord|2735255|2737302|ecoli_W3110|W3110}}  
W3110: 2736255..2736302<br /><gbrowseImage>
name=NC_007779:2736255..2736302
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2735255|2737302|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2735255..2737302 GBrowse(W3110)]
{{GBrowseFastaLink|W3110|NC_007779|2736255|2736302|FASTA Dump}}
|-  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2736255..2736302&plugin_action=Go FASTA Dump]
[[DH10B]]
|-class='sortbottom'
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|
DH10B: 2827386..2827433<br /><gbrowseImage>
name=NC_010473:2827386..2827433
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2827292|2827527|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2827292|2827527|FASTA Dump}}
 
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===Notes===
===Notes===
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|- {{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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{|class = 'sortable' {{Prettytable}} id='140493'
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|- {{table_heading_style}}
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!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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&Delta;pheL (Keio:JW2579)
&Delta;pheL (Keio:JW2579)
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|
|
[[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=108328 CGSC10047]<ref name='LIB:cgsc'/>  
|
|-
|
''&#916;pheL761::kan''
|
 
|
 
|
 
|
 
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
PMID:16738554
|
[[cgscmutation:102320|CGSC:102320]]
|
|
   
   
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15765.B4e04c0fd200d2-->
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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:  
|-
|-
|
[[:Category:Kohara_Phage:21D7|21D7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=437 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:E8F2|E8F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=438 Genobase]
|
PMID:3038334
|-  
|
|
[[nadB:Gene|nadB51::Tn10]]
[[nadB:Gene|nadB51::Tn10]]
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|
|
est. P1 cotransduction: 37% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 37% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
[[pheA:Gene|pheA18::Tn10]]
[[pheA:Gene|pheA18::Tn10]]
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|
|
est. P1 cotransduction: 94% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 94% <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='140495'
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:EG11271
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:EG11271
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11271 EcoCyc:EG11271] 
RegulonDB:ECK120001245
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1250 EchoBASE:EB1250]
[http://www.ncbi.nlm.nih.gov/gene?term=947080 GeneID:947080]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2598 EcoliGenExpDB:b2598] 
EchoBASE:EB1250
|
|
''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=EG11271 EcoGene:EG11271] 
ASAP:ABE-0008543
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[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:phe genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:43, 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

pheL

Mnemonic

Phenylalanine

Synonyms

ECK2595, b2598, JW2579, pheAE[1], pheAE

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

58.96 minutes 

MG1655: 2735621..2735668
<gbrowseImage> name=NC_000913:2735621..2735668 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2659007..2659054
<gbrowseImage> name=NC_012967:2659007..2659054 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2621433..2621480
<gbrowseImage> name=NC_012759:2621433..2621480 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2736255..2736302
<gbrowseImage> name=NC_007779:2736255..2736302 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2827386..2827433
<gbrowseImage> name=NC_010473:2827386..2827433 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

ΔpheL (Keio:JW2579)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10047[3]

ΔpheL761::kan

PMID:16738554[2]

CGSC:102320


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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[4]

Status:

Primer 1:

Primer 2:

21D7

Kohara Phage

Genobase

PMID:3038334[5]

E8F2

Kohara Phage

Genobase

PMID:3038334[5]

nadB51::Tn10

Linked marker

CAG18480 = CGSC7419[3]

est. P1 cotransduction: 37% [6]

pheA18::Tn10

Linked marker

CAG12158 = CGSC7421[3]

est. P1 cotransduction: 94% [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

EcoCyc

EcoCyc:EG11271

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11271

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001245

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947080

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1250

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008543

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. ↑ 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. ↑ 5.0 5.1 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
  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).

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