ysdC:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
imported>Wikientrybot
No edit summary
Line 27: Line 27:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"
 
|-
|-
!{{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'/>
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.O46a9fc2c4e2e0&page=17919&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.O46a9fc2c4e2e0&page=17919&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.O46a9fc2c4e2e0-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.O46a9fc2c4e2e0-->
Line 59: Line 61:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' {{Prettytable}} id='146961'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{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
Line 80: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|3859196|3859372|FASTA Dump}}
{{GBrowseFastaLink|ecoli|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
Line 91: Line 93:
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3779066|3779242|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3779066|3779242|FASTA Dump}}  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.J46a9fc2cd061d&page=17919&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.J46a9fc2cd061d&page=17919&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.J46a9fc2cd061d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.J46a9fc2cd061d-->
Line 105: Line 108:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='146962'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Feature type!!Location!!Description
!|Feature type!!Location!!Description
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.V46a9fc2d94ea6&page=17919&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.V46a9fc2d94ea6&page=17919&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.V46a9fc2d94ea6-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.V46a9fc2d94ea6-->
Line 126: Line 130:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' {{Prettytable}} id='146963'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
|- {{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
|-
|-  
|
|
&Delta;ysdC (Keio:JW5937)
&Delta;ysdC (Keio:JW5937)
Line 144: Line 148:
|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[PMID:16738554]]<ref name=PMID:16738554/>
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
|
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.M46a9fc2ddf324&page=17919&pagename={{FULLPAGENAMEE}} edit table] || || || || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.M46a9fc2ddf324&page=17919&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.M46a9fc2ddf324-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.M46a9fc2ddf324-->
Line 164: Line 168:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' {{Prettytable}} id='146964'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-
|-  
|
|


Line 178: Line 182:
|
|
[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]]<ref name=PMID:16769691/>


Status:
Status:
Line 186: Line 189:


Primer 2:  
Primer 2:  
|-
|-  
|
|
zic-4901::Tn10
zic-4901::Tn10
Line 195: Line 198:
|
|
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 29% <ref name='LIB:Nichols_linked_Tn'/>  
|-
|-  
|
|
zid-501::Tn10
zid-501::Tn10
Line 204: Line 207:
|
|
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 59% <ref name='LIB:Nichols_linked_Tn'/>  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.C46a9fc2ea29fa&page=17919&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.C46a9fc2ea29fa&page=17919&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.C46a9fc2ea29fa-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.C46a9fc2ea29fa-->
Line 218: Line 222:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' {{Prettytable}} id='146965'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10564 EcoCyc:G0-10564]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10564 EcoCyc:G0-10564]
|
|
   
   
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.L46a9fc2f61bcf&page=17919&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.L46a9fc2f61bcf&page=17919&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.L46a9fc2f61bcf-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.L46a9fc2f61bcf-->
Line 246: Line 251:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **  
*
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' {{Prettytable}} id='99786'
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!Name!!URL!!Comments
!|Name!!URL!!Comments
 
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.E46a71673d7238&page=17919&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17919.E46a71673d7238&page=17919&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.E46a71673d7238-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.17919.E46a71673d7238-->

Revision as of 18:52, 29 January 2009

{{#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 Alleles and Phenotypes 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

ysdC

Mnemonic
Synonyms

ECK3672, b4556, JW5937[1]

edit table

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

83.18 minutes, 83.18 minutes 

MG1655: 3859372..3859196
gbrowse_img.php?coord=3858196..3860372&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3779066..3779242
gbrowse_img.php?coord=3778066..3780242&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit table

See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature type Location Description
edit table

See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Notes

Alleles and Phenotypes

[back to top]


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


edit table

See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Notes

Genetic Resources

[back to top]


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:

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: 29% [5]

zid-501::Tn10

Linked marker

CAG18499 = CGSC7458[4]

est. P1 cotransduction: 59% [5]

edit table

See Help:Gene_resources for help entering information into the Genetic Resources table.

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc (EcoliWiki Page)

EcoCyc:G0-10564


edit table

See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Notes

Links

[back to top]


Name URL Comments
edit table

See Help:Links_table for how to enter or edit information in this section of EcoliWiki.

References

[back to top]


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. ↑ 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. ↑ 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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ysdC:Gene&oldid=664789"