ysdC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ysdC}}{{Tab On|Gene|ysdC}}{{Tab|Gene Product(s)|ysdC}}{{Tab|Expression|ysdC}}{{Tab|Evolution|ysdC}}{{Tab|On One Page|ysdC}}{{TabsBottom}}
{{Tab|Quickview|ysdC}}{{Tab On|Gene|ysdC}}{{Tab|Gene Product(s)|ysdC}}{{Tab|Expression|ysdC}}{{Tab|Evolution|ysdC}}{{Tab|On One Page|ysdC}}{{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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{|  id="O46a9fc2c4e2e0"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ysdC''  
''ysdC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3672, b4556, JW5937''<ref name='LIB:Riley_2006'/>
''ECK3672, b4556, JW5937''<ref name='LIB:Riley_2006'/>
|-
 
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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="J46a9fc2cd061d"  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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83.18 minutes, 83.18 minutes&nbsp;
83.18 minutes, 83.18 minutes&nbsp;
|
|
MG1655: 3859372..3859196<br />{{GBrowseFigureByCoord|3858196|3860372|ecoli|MG1655}}
MG1655: 3859372..3859196<br /><gbrowseImage>
name=NC_000913:3859196..3859372
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10564 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10564 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3858196..3860372 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3858196|3860372|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3859196..3859372&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3859196|3859372|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10564 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10564 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3779066..3779242<br />{{GBrowseFigureByCoord|3778066|3780242|ecoli_W3110|W3110}}
W3110: 3779066..3779242<br /><gbrowseImage>
name=NC_007779:3779066..3779242
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3778066..3780242 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|3778066|3780242|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3779066..3779242&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|3779066|3779242|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="V46a9fc2d94ea6"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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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="M46a9fc2ddf324"  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;ysdC (Keio:JW5937)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
|-class='sortbottom'
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|
 
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:
 
Primer 1:
 
Primer 2:
|-
|
[[:Category:Kohara_Phage:8E8|8E8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=567 Genobase]
|
PMID:3038334
|-
|
zic-4901::Tn10
|
Linked marker
|
CAG18492 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38944 CGSC7457]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
zid-501::Tn10
|
Linked marker
|
CAG18499 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38945 CGSC7458]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9fc2f61bcf"  class=" tableEdit Gene_accessions_table" 
|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EcoGene]]
|
EcoGene:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120026455
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[[EchoBASE]]
|
EchoBASE:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[ASAP]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10564 EcoCyc:G0-10564] 
ASAP:
|
|
''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:ysd genes]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:49, 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

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ysdC

Mnemonic
Synonyms

ECK3672, b4556, JW5937[1]

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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

83.18 minutes, 83.18 minutes 

MG1655: 3859372..3859196
<gbrowseImage> name=NC_000913:3859196..3859372 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3779066..3779242
<gbrowseImage> name=NC_007779:3779066..3779242 source=W3110 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

ΔysdC (Keio:JW5937)

deletion

deletion

PMID:16738554[2]

Shigen


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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[3]

Status:

Primer 1:

Primer 2:

8E8

Kohara Phage

Genobase

PMID:3038334[4]

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[5]

est. P1 cotransduction: 29% [6]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[5]

est. P1 cotransduction: 59% [6]

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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:

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026455

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

References

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  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 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. ↑ 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
  4. ↑ 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
  5. ↑ 5.0 5.1 CGSC: The Coli Genetics Stock Center
  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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