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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
|
||
''rydB''  
''rydB''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Systematic nomenclature
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1681, b4430, JWR0236, IS082, tpe7''<ref name='LIB:Riley_2006'/>, tpe7''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13937.U46a9cc8487208&page=13937&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1681, b4430, JWR0236, IS082, tpe7''<ref name='LIB:Riley_2006'/>
|-
|colspan='2'|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79.13937.U46a9cc8487208&page=13937&pagename={{FULLPAGENAMEE}} edit table]
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<!--Nomenclature_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="F46a9cc850e9b0"  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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37.99 minutes&nbsp;
37.99 minutes&nbsp;
|
|
MG1655: 1762804..1762737<br />{{GBrowseFigureByCoord|1761737|1763804|ecoli|MG1655}}
MG1655: 1762804..1762737<br /><gbrowseImage>
name=NC_000913:1762737..1762804
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-8876 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-8876 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1761737..1763804 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1761737|1763804|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1762737..1762804&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1762737|1762804|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-8876 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-8876 EcoCyc Sequence Dump]  
|-
|-
|
[[BW2952]]
|
 
|
NC_012759: 1654796..1654863<br /><gbrowseImage>
name=NC_012759:1654796..1654863
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1654796|1654863|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|1654796|1654863|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1766494..1766427<br />{{GBrowseFigureByCoord|1765427|1767494|ecoli_W3110|W3110}}  
W3110: 1766494..1766427<br /><gbrowseImage>
name=NC_007779:1766427..1766494
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1765427|1767494|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1766427|1766494|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1853375..1853308<br /><gbrowseImage>
name=NC_010473:1853308..1853375
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1765427..1767494 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1853174|1853509|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1766427..1766494&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1853174|1853509|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="G46a9cc85b40c6"  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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====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="H46a9cc8602d23"  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;rydB (Keio:)
|
deletion
|
deletion
|
 
|


|
|- class="tableEdit_footer"
[[PMID:16738554]]<ref name=PMID:16738554/>
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13937.H46a9cc8602d23&page=13937&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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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.13937.H4e04c372be656-->
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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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[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:15G10|15G10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=320 Genobase]
|
PMID:3038334
|-  
|
|
[[yddE:Gene|zdd-235::Tn10]]
[[yddE:Gene|zdd-235::Tn10]]
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CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zdc-235::Tn10  
Synonyms:zdc-235::Tn10  
|-
|-  
|
|
zdi-925::Tn10
zdi-925::Tn10
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CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 61% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 61% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdh-925::Tn10


Synonyms:zdh-925::Tn10
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!Database!!Accession!!Notes
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[[EcoCyc]]
|
EcoCyc:G0-8876
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=2847670 GeneID:2847670]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[RegulonDB]]
|
RegulonDB:ECK120002588
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-8876 EcoCyc:G0-8876] 
EchoBASE:EB4514
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[ASAP]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4514 EchoBASE:EB4514] 
ASAP:ABE-0047250
|
|
''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:ryd genes]]

Latest revision as of 20:38, 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

rydB

Mnemonic

Systematic nomenclature

Synonyms

ECK1681, b4430, JWR0236, IS082, tpe7[1], tpe7

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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

37.99 minutes 

MG1655: 1762804..1762737
<gbrowseImage> name=NC_000913:1762737..1762804 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1654796..1654863
<gbrowseImage> name=NC_012759:1654796..1654863 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1766494..1766427
<gbrowseImage> name=NC_007779:1766427..1766494 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1853375..1853308
<gbrowseImage> name=NC_010473:1853308..1853375 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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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[2]

Status:

Primer 1:

Primer 2:

15G10

Kohara Phage

Genobase

PMID:3038334[3]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: % [5]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[4]

est. P1 cotransduction: 61% [5]
Synonyms:zdh-925::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:G0-8876

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:2847670

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002588

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4514

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0047250

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. ↑ 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).

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