aroE:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|aroE}}{{Tab On|Gene|aroE}}{{Tab|Gene Product(s)|aroE}}{{Tab|Expression|aroE}}{{Tab|Evolution|aroE}}{{Tab|On One Page|aroE}}{{TabsBottom}}
{{Tab|Quickview|aroE}}{{Tab On|Gene|aroE}}{{Tab|Gene Product(s)|aroE}}{{Tab|Expression|aroE}}{{Tab|Evolution|aroE}}{{Tab|On One Page|aroE}}{{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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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''aroE''  
''aroE''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Aromatic
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3268, b3281, JW3242''<ref name='LIB:Riley_2006'/>, JW3242''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17111.I46a9f1ff2d4c2&page=17111&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3268, b3281, JW3242''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
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<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="R46a9f1ffae1e5"  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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73.89 minutes, 73.89 minutes&nbsp;
73.89 minutes, 73.89 minutes&nbsp;
|
|
MG1655: 3428860..3428042<br />{{GBrowseFigureByCoord|3427042|3429860|ecoli|MG1655}}
MG1655: 3428860..3428042<br /><gbrowseImage>
name=NC_000913:3428042..3428860
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10077 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10077 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3427042..3429860 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3427042|3429860|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3428042..3428860&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3428042|3428860|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10077 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10077 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3358743..3357925<br /><gbrowseImage>
name=NC_012967:3357925..3358743
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3357925|3358743|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|3357925|3358743|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3315199..3316017<br /><gbrowseImage>
name=NC_012759:3315199..3316017
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3315199|3316017|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3315199|3316017|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4209578..4210396<br />{{GBrowseFigureByCoord|4208578|4211396|ecoli_W3110|W3110}}  
W3110: 4209578..4210396<br /><gbrowseImage>
name=NC_007779:4209578..4210396
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4208578|4211396|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|4209578|4210396|FASTA Dump}}  
|-
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4208578..4211396 GBrowse(W3110)]  
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4209578..4210396&plugin_action=Go FASTA Dump]
 
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DH10B: 3526605..3525787<br /><gbrowseImage>
name=NC_010473:3525787..3526605
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3524151|3528241|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3524151|3528241|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
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[[MG1655]]
|
3428042
|
Edman degradation
|
PMID:3277621<br />
|
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9f200b6ea0"  class=" tableEdit Gene_allele_table dataTable" 
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!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
|-class='sortbottom'
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''aroE(del)'' (Keio:JW3242)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br />[http://cgsc2.biology.yale.edu/Strain.php?ID=99783 CGSC8307]<ref name='LIB:cgsc'/>
|
|-
|
''aroE24''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:6187|CGSC:6187]]
|
|-
|
''aroE353''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:7564|CGSC:7564]]
|
|-
|
''aroE721(del)''::kan
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:99781|CGSC:99781]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3242
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCGAAACCTATGCTGTTTTTGG
 
Primer 2:CCgGCGGACAATTCCTCCTGCAA
|-
|
[[acrF:Gene|acrF3083::Tn10]]
|
Linked marker
|
CAG12075 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40247 CGSC7447]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 63% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10
|-
|
[[smg:Gene|smg-3082::Tn10]]
|
Linked marker
|
CAG12071 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40240 CGSC7444]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 98% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
 
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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}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10077 EcoCyc:EG10077] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0075 EchoBASE:EB0075] 
EcoCyc:EG10077
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3281 EcoliGenExpDB:b3281] 
EcoGene:EG10077
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4042 ECOL199310CYC:C4042] 
RegulonDB:ECK120000073
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|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=EG10077 EcoGene:EG10077]
[http://www.ncbi.nlm.nih.gov/gene?term=947776 GeneID:947776]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=AROE ECOO157CYC:AROE] 
EchoBASE:EB0075
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1004 CGSC:1004] 
ASAP:ABE-0010763
|
|
''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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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:aro genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:46, 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

aroE

Mnemonic

Aromatic

Synonyms

ECK3268, b3281, JW3242[1], JW3242

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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

73.89 minutes, 73.89 minutes 

MG1655: 3428860..3428042
<gbrowseImage> name=NC_000913:3428042..3428860 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3358743..3357925
<gbrowseImage> name=NC_012967:3357925..3358743 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3315199..3316017
<gbrowseImage> name=NC_012759:3315199..3316017 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4209578..4210396
<gbrowseImage> name=NC_007779:4209578..4210396 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3526605..3525787
<gbrowseImage> name=NC_010473:3525787..3526605 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

Coding Start (SO:0000323)

MG1655

3428042

Edman degradation

PMID:3277621[2]


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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

aroE(del) (Keio:JW3242)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC8307[4]

aroE24

CGSC:6187

aroE353

CGSC:7564

aroE721(del)::kan

PMID:16738554[3]

CGSC:99781


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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

JW3242

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGAAACCTATGCTGTTTTTGG

Primer 2:CCgGCGGACAATTCCTCCTGCAA

acrF3083::Tn10

Linked marker

CAG12075 = CGSC7447[4]

est. P1 cotransduction: 63% [6]
Synonyms:zhd-3083::Tn10, zhe-3083::Tn10

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[4]

est. P1 cotransduction: 98% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

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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:EG10077

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10077

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000073

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947776

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0075

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0010763

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. ↑ Anton, IA & Coggins, JR (1988) Sequencing and overexpression of the Escherichia coli aroE gene encoding shikimate dehydrogenase. Biochem. J. 249 319-26 PubMed
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  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 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

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