araE: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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*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
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{|   id="U46a9e79bb56df" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''araE''  
''araE''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Arabinose
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK2839, b2841, JW2809''<ref name='LIB:Riley_2006'/>
''ECK2839, b2841, JW2809''<ref name='LIB:Riley_2006'/>, JW2809''


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*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="T46a9e79c3fea3"  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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64.2 minutes&nbsp;
64.2 minutes&nbsp;
|
|
MG1655: 2980204..2978786<br />{{GBrowseFigureByCoord|2977786|2981204|ecoli|MG1655}}
MG1655: 2980204..2978786<br /><gbrowseImage>
name=NC_000913:2978786..2980204
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10056 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10056 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|2977786|2981204|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|2977786|2981204|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|2978786|2980204|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|2978786|2980204|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10056 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10056 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 2876803..2875385<br /><gbrowseImage>
name=NC_012967:2875385..2876803
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|2875385|2876803|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2875385|2876803|FASTA Dump}}
|-
|
[[BW2952]]
|
|
NC_012759: 2865934..2867352<br /><gbrowseImage>
name=NC_012759:2865934..2867352
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|NC_012759|2865934|2867352|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2865934|2867352|FASTA Dump}}
|-  
|-  
|
|
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&nbsp;
&nbsp;
|
|
W3110: 2980838..2979420<br />{{GBrowseFigureByCoord|2978420|2981838|ecoli_W3110|W3110}}
W3110: 2980838..2979420<br /><gbrowseImage>
name=NC_007779:2979420..2980838
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|2978420|2981838|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|2978420|2981838|GBrowse(W3110)}}  
|
{{GBrowseFastaLink|W3110|NC_007779|2979420|2980838|FASTA Dump}}
|-
|
[[DH10B]]
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|2979420|2980838|FASTA Dump}}


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DH10B: 3074074..3072656<br /><gbrowseImage>
name=NC_010473:3072656..3074074
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3069820|3076910|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3069820|3076910|FASTA Dump}}
 
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****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9e79d42ea4"  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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|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009319 araE::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009319 araE::Tn5KAN-I-SceI] (FB20957)
|
|
 
Insertion at nt 940 in Plus orientation
|
|


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|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20957]
|
|
At position 940 in Plus orientation, does not contain plasmid  [[pKD46]].<br />ASAP strain name: FB20957
does not contain [[pKD46]]  
|-  
|-  
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009319 araE::Tn5KAN]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0009319 araE::Tn5KAN-I-SceI] (FB20958)
|
|
 
Insertion at nt 940 in Plus orientation
|
|


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|
|
PMID:12519969
PMID:15262929
|
|
[[asapstrains:ASAP|ASAP]]
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20958]
|
|
At position 940 in Plus orientation, contains plasmid  [[pKD46]].<br />ASAP strain name: FB20958
contains [[pKD46]]  
|-  
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|
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16253.A4e04b76f55e77-->
<!--
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A4e04b76f55e77"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGACGCCGATATTTCTCAACTT  
Primer 2:CCGACGCCGATATTTCTCAACTT  
|-
|
[[:Category:Kohara_Phage:8H3|8H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=462 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:12H3|12H3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=463 Genobase]
|
PMID:3038334
|-  
|-  
|
|
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Synonyms:zgd-210::Tn10, zgf-210::Tn10  
Synonyms:zgd-210::Tn10, zgf-210::Tn10  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10056 EcoCyc:EG10056]
EcoCyc:EG10056
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0054 EchoBASE:EB0054]
EcoGene:EG10056
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2841 EcoliGenExpDB:b2841]
RegulonDB:ECK120000052
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3438 ECOL199310CYC:C3438]
[http://www.ncbi.nlm.nih.gov/gene?term=947341 GeneID:947341]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10056 EcoGene:EG10056]
EchoBASE:EB0054
|
|
''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=ARAE ECOO157CYC:ARAE]
ASAP:ABE-0009319
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/1024 CGSC:1024]
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0009319&formSubmitReturn=1 ASAP:ABE-0009319]
|


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
Line 431: Line 516:
[[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:ara genes]][[Category:Gene_List:DH10B]]
[[Category:ara genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:44, 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

araE

Mnemonic

Arabinose

Synonyms

ECK2839, b2841, JW2809[1], JW2809

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

64.2 minutes 

MG1655: 2980204..2978786
<gbrowseImage> name=NC_000913:2978786..2980204 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2876803..2875385
<gbrowseImage> name=NC_012967:2875385..2876803 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2865934..2867352
<gbrowseImage> name=NC_012759:2865934..2867352 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2980838..2979420
<gbrowseImage> name=NC_007779:2979420..2980838 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3074074..3072656
<gbrowseImage> name=NC_010473:3072656..3074074 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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Allele Nt change(s) AA change(s) Phenotype: Type Phenotype: Description Reference Availability Comments

ΔaraE (Keio:JW2809)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10196[3]

araE::Tn5KAN-I-SceI (FB20957)

Insertion at nt 940 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20957

does not contain pKD46

araE::Tn5KAN-I-SceI (FB20958)

Insertion at nt 940 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20958

contains pKD46

araE452

CGSC:80477

araE455

CGSC:80479

araE79

CGSC:80486

ΔaraE766::kan

PMID:16738554[2]

CGSC:100024


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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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Resource Resource Type Source Notes/Reference

JW2809

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCGTTACTATCAATACGGAATC

Primer 2:CCGACGCCGATATTTCTCAACTT

8H3

Kohara Phage

Genobase

PMID:3038334[6]

12H3

Kohara Phage

Genobase

PMID:3038334[6]

recD1901::Tn10

Linked marker

CAG12135 = CGSC7429[3]

est. P1 cotransduction: 34% [7]

speA210::Tn10

Linked marker

CAG12168 = CGSC7431[3]

est. P1 cotransduction: % [7]
Synonyms:zgd-210::Tn10, zgf-210::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:EG10056

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10056

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000052

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947341

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0054

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009319

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  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. ↑ 4.0 4.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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
  7. ↑ 7.0 7.1 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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