yddK:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|yddK}}{{Tab On|Gene|yddK}}{{Tab|Gene Product(s)|yddK}}{{Tab|Expression|yddK}}{{Tab|Evolution|yddK}}{{Tab|On One Page|yddK}}{{TabsBottom}}
{{Tab|Quickview|yddK}}{{Tab On|Gene|yddK}}{{Tab|Gene Product(s)|yddK}}{{Tab|Expression|yddK}}{{Tab|Evolution|yddK}}{{Tab|On One Page|yddK}}{{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
|
||
''yddK''  
''yddK''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1465, b1471, JW1467''<ref name='LIB:Riley_2006'/>
''ECK1465, b1471, JW1467''<ref name='LIB:Riley_2006'/>, JW1467''
|-
 
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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==
{{BacktoTop}}
<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="T46a9c7be09a65"  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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33.25 minutes&nbsp;
33.25 minutes&nbsp;
|
|
MG1655: 1543738..1542782<br />{{GBrowseFigureByCoord|1541782|1544738|ecoli|MG1655}}
MG1655: 1543738..1542782<br /><gbrowseImage>
name=NC_000913:1542782..1543738
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6772 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6772 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1541782..1544738 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1541782|1544738|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1542782..1543738&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1542782|1543738|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6772 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6772 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 1519865..1518909<br /><gbrowseImage>
name=NC_012967:1518909..1519865
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1518909|1519865|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1518909|1519865|FASTA Dump}}
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1547428..1546472<br />{{GBrowseFigureByCoord|1545472|1548428|ecoli_W3110|W3110}}  
W3110: 1547428..1546472<br /><gbrowseImage>
name=NC_007779:1546472..1547428
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1545472|1548428|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1546472|1547428|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1634333..1633377<br /><gbrowseImage>
name=NC_010473:1633377..1634333
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1545472..1548428 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1631465|1636245|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1546472..1547428&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1631465|1636245|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9c7bead252"  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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==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="Z46a9c7beef95d"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;yddK (Keio:JW1467)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107558 CGSC9277]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;yddK764::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:104210|CGSC:104210]]
|
 
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13507.N4e04c7adbcdbd-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N4e04c7adbcdbd"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|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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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9c7bf9f39c"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW1467
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCATCACTGACCTTATATTACA
 
Primer 2:CCAGTTTTGCTCTGTTTTATTAT
|-
|
[[:Category:Kohara_Phage:1G4|1G4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=276 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:1G9|1G9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=277 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:9B8|9B8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=278 Genobase]
|
PMID:3038334
|-
|
[[yddE:Gene|zdd-235::Tn10]]
|
Linked marker
|
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 79% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdc-235::Tn10
|-
|
zdi-925::Tn10
|
Linked marker
|
CAG12151 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39862 CGSC7385]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdh-925::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|
[[EcoCyc]]
|
EcoCyc:G6772
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6772 EcoCyc:G6772] 
EcoGene:EG13782
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3544 EchoBASE:EB3544] 
RegulonDB:ECK120003361
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1471 EcoliGenExpDB:b1471]
[http://www.ncbi.nlm.nih.gov/gene?term=947312 GeneID:947312]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13782 EcoGene:EG13782] 
EchoBASE:EB3544
|
|
''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=Z2242 ECOO157CYC:Z2242] 
ASAP:ABE-0004906
|
|
''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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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ydd genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:29, 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

yddK

Mnemonic
Synonyms

ECK1465, b1471, JW1467[1], JW1467

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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

33.25 minutes 

MG1655: 1543738..1542782
<gbrowseImage> name=NC_000913:1542782..1543738 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1519865..1518909
<gbrowseImage> name=NC_012967:1518909..1519865 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1547428..1546472
<gbrowseImage> name=NC_007779:1546472..1547428 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1634333..1633377
<gbrowseImage> name=NC_010473:1633377..1634333 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

ΔyddK (Keio:JW1467)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9277[3]

ΔyddK764::kan

PMID:16738554[2]

CGSC:104210


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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

JW1467

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCATCACTGACCTTATATTACA

Primer 2:CCAGTTTTGCTCTGTTTTATTAT

1G4

Kohara Phage

Genobase

PMID:3038334[5]

1G9

Kohara Phage

Genobase

PMID:3038334[5]

9B8

Kohara Phage

Genobase

PMID:3038334[5]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[3]

est. P1 cotransduction: 79% [6]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[3]

est. P1 cotransduction: % [6]
Synonyms:zdh-925::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:G6772

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13782

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003361

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947312

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3544

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004906

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 5.2 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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