rhaD: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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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''rhaD''  
''rhaD''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Rhamnose
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3895, b3902, JW3873''<ref name='LIB:Riley_2006'/>, JW3873''


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!{{table_heading_style}} |Synonyms
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''ECK3895, b3902, JW3873''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<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="Y46aa01d3192ce"  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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MG1655
MG1655
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88.18 minutes, 88.18 minutes&nbsp;
88.18 minutes, 88.18 minutes&nbsp;
|
|
MG1655: 4092295..4091471<br />{{GBrowseFigureByCoord|4090471|4093295|ecoli|MG1655}}
MG1655: 4092295..4091471<br /><gbrowseImage>
name=NC_000913:4091471..4092295
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11866 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11866 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4090471..4093295 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4090471|4093295|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4091471..4092295&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4091471|4092295|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11866 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11866 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4074030..4073206<br /><gbrowseImage>
name=NC_012967:4073206..4074030
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4073206|4074030|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4073206|4074030|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3981140..3981964<br /><gbrowseImage>
name=NC_012759:3981140..3981964
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3981140|3981964|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3981140|3981964|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3542409..3543233<br />{{GBrowseFigureByCoord|3541409|3544233|ecoli_W3110|W3110}}  
W3110: 3542409..3543233<br /><gbrowseImage>
name=NC_007779:3542409..3543233
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3541409|3544233|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|3542409|3543233|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 4191992..4191168<br /><gbrowseImage>
name=NC_010473:4191168..4191992
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3541409..3544233 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4189520|4193640|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3542409..3543233&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4189520|4193640|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="J46aa01d3d2c18"  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
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<protect><!--Sequence_notes--></protect>
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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="I46aa01d429431"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!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;rhaD (Keio:)
|
deletion
|
deletion
|
 
|


|
|- class="tableEdit_footer"
[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen] 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46aa01d4e312f"  class=" tableEdit Gene_resource_table" 
|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3873
JW3873
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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:Clone OK
Status:Clone OK
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Primer 2:CCaAGCGCCAGCGCACTGGCGAG  
Primer 2:CCaAGCGCCAGCGCACTGGCGAG  
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[[:Category:Kohara_Phage:4B6|4B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=541 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7G8|7G8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=542 Genobase]
|
PMID:3038334
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[[yihO:Gene|zih-35::Tn10]]
|
Linked marker
|
CAG18495 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37140 CGSC7467]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[pflD:Gene|pflD501::Tn10]]
|
Linked marker
|
CAG18477 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37152 CGSC7470]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).
 
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===Notes===
===Notes===
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11866 EcoCyc:EG11866] 
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1812 EchoBASE:EB1812] 
EcoCyc:EG11866
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3902 EcoliGenExpDB:b3902] 
EcoGene:EG11866
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C4851 ECOL199310CYC:C4851] 
RegulonDB:ECK120001797
|
|
''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]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG11866 EcoGene:EG11866]
[http://www.ncbi.nlm.nih.gov/gene?term=948401 GeneID:948401]
|
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=RHAD ECOO157CYC:RHAD] 
EchoBASE:EB1812
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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|
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/289 CGSC:289] 
ASAP:ABE-0012731
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===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:rha genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 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

rhaD

Mnemonic

Rhamnose

Synonyms

ECK3895, b3902, JW3873[1], JW3873

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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

88.18 minutes, 88.18 minutes 

MG1655: 4092295..4091471
<gbrowseImage> name=NC_000913:4091471..4092295 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4074030..4073206
<gbrowseImage> name=NC_012967:4073206..4074030 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3981140..3981964
<gbrowseImage> name=NC_012759:3981140..3981964 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3542409..3543233
<gbrowseImage> name=NC_007779:3542409..3543233 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4191992..4191168
<gbrowseImage> name=NC_010473:4191168..4191992 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

JW3873

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCCAAAACATTACTCAGTCCTG

Primer 2:CCaAGCGCCAGCGCACTGGCGAG

4B6

Kohara Phage

Genobase

PMID:3038334[3]

7G8

Kohara Phage

Genobase

PMID:3038334[3]

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[4]

est. P1 cotransduction: 35% [5]

pflD501::Tn10

Linked marker

CAG18477 = CGSC7470[4]

est. P1 cotransduction: 9% [5]
Synonyms:zij-501::Tn10 nnnCAG18477 also carries metF79(Am) (CGSC).

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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:EG11866

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11866

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001797

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948401

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1812

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012731

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. ↑ 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
  3. ↑ 3.0 3.1 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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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