rep:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Edited by wikibot
imported>Wikientrybot
Move help links into the <above> tag inside templates.
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
|
||
''rep''  
''rep''  
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
|-
 
|colspan='2'|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.X46a9feac3337d&page=18115&pagename={{FULLPAGENAMEE}} edit table]
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.X46a9feac3337d&page=18115&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.X46a9feac3337d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.X46a9feac3337d-->
{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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='147549'
{|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|3958700|3960721|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|3958700|3960721|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10837 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10837 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
Line 91: Line 93:
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3673983|3676004|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|AC_000091|3673983|3676004|FASTA Dump}}  
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.N46a9feacb6204&page=18115&pagename={{FULLPAGENAMEE}} edit table] || || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.N46a9feacb6204&page=18115&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.N46a9feacb6204-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.N46a9feacb6204-->
{{Gene_location_help}}
 
<!--Location_notes--></protect>
<!--Location_notes--></protect>
===Notes===
===Notes===
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='147550'
{|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=421aa90e079fa326b6494f812ad13e79.18115.I46a9fead7adba&page=18115&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.I46a9fead7adba&page=18115&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.I46a9fead7adba-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.I46a9fead7adba-->
{{Gene_sequence_features_help}}
 
<protect><!--Sequence_notes--></protect>
<protect><!--Sequence_notes--></protect>
====Notes====
====Notes====
Line 129: Line 133:
*  ** 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' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}  
{|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}}
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]
Line 178: Line 181:
|
|


|
|[[PMID:383240]]<ref name=PMID:383240/>
[[PMID:383240]]<ref name=PMID:383240/>
|
|
[[cgscmutation:9794|CGSC:9794]]
[[cgscmutation:9794|CGSC:9794]]
Line 212: Line 214:
|
|


|
|[[PMID:6286604]]<ref name=PMID:6286604/>
[[PMID:6286604]]<ref name=PMID:6286604/>
|
|
[[cgscmutation:90823|CGSC:90823]]
[[cgscmutation:90823|CGSC:90823]]
Line 229: Line 230:
|
|


|
|[[PMID:16738554]]<ref name=PMID:16738554/>
[[PMID:16738554]]<ref name=PMID:16738554/>
|
|
[[cgscmutation:113537|CGSC:113537]]
[[cgscmutation:113537|CGSC:113537]]
Line 240: Line 240:
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.Y46a9feadc506b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.Y46a9feadc506b-->
{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===
Line 250: Line 250:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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='147552'
{|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
|-
|-  
|
|
JW5604
JW5604
Line 264: Line 264:
|
|
[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:cloned as old JW
Status:cloned as old JW
Line 272: Line 271:


Primer 2:CCTTTCCCTCGTTTTGCCGCCAT  
Primer 2:CCTTTCCCTCGTTTTGCCGCCAT  
|-
|-  
|
|
[[ilvD:Gene|ilvD500::Tn10]]
[[ilvD:Gene|ilvD500::Tn10]]
Line 280: Line 279:
CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
CAG18431 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40338 CGSC7462]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 83% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 83% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:ilv500::Tn10  
 
|-  
Synonyms:ilv500::Tn10  
|-
|
|
metEo-3079::Tn10
metEo-3079::Tn10
Line 291: Line 288:
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
CAG18491 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40350 CGSC7464]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 10% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
 
Synonyms:metE3079::Tn10  
 


The Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.
|-class='sortbottom'
|-class='sortbottom'
|[{{SERVER}}{{SCRIPTPATH}}/index.php?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.D46a9feae893d7&page=18115&pagename={{FULLPAGENAMEE}} edit table] || || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.D46a9feae893d7&page=18115&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.D46a9feae893d7-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.D46a9feae893d7-->
{{Gene_resources_help}}
 
<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
Line 314: Line 307:
*  ** 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' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|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}}
Line 371: Line 364:
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012344&formSubmitReturn=1 ASAP:ABE-0012344]
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0012344&formSubmitReturn=1 ASAP:ABE-0012344]
|
|
   
   
Line 379: Line 372:
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.J46a9feaf34a80-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.J46a9feaf34a80-->
{{Gene_accessions_help}}
 
<protect><!--Gene_accessions_notes--></protect>
<protect><!--Gene_accessions_notes--></protect>
===Notes===
===Notes===
Line 389: Line 382:
<!--
<!--
******************************************************************************************
******************************************************************************************
*
*  
*  ** 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='99884'
{|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=421aa90e079fa326b6494f812ad13e79.18115.G46a718b356745&page=18115&pagename={{FULLPAGENAMEE}} edit table] || ||
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18115.G46a718b356745&page=18115&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.G46a718b356745-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18115.G46a718b356745-->
{{Links_help}}
 


<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
 
<references/>
<references/>
__NOTOC__
__NOTOC__

Revision as of 21:35, 21 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

rep

Mnemonic
Synonyms

ECK3770, b3778, JW5604, dasC, mbrA, mmrA, dasC?[1][2]

edit 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

85.32 minutes 

MG1655: 3958700..3960721
gbrowse_img.php?coord=3957700..3961721&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 3676004..3673983
gbrowse_img.php?coord=3672983..3677004&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

edit 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


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

Δrep (Keio:JW5604)

deletion

deletion

PMID:16738554[3]

Shigen

rep-5

CGSC:7013

rep-3

PMID:383240[4]

CGSC:9794

rep-142(ts)

temperature sensitive

CGSC:90737

[rep-71]

PMID:6286604[5]

CGSC:90823

null allele

Δrep-729::kan

PMID:16738554[3]

CGSC:113537


edit table


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

JW5604

Plasmid clone

Shigen

PMID:16769691[6]

Status:cloned as old JW

Primer 1:GCCCGTCTAAACCCCGGCCAACA

Primer 2:CCTTTCCCTCGTTTTGCCGCCAT

ilvD500::Tn10

Linked marker

CAG18431 = CGSC7462[7]

est. P1 cotransduction: 83% [8]nnSynonyms:ilv500::Tn10

metEo-3079::Tn10

Linked marker

CAG18491 = CGSC7464[7]

est. P1 cotransduction: 10% [8]nnSynonyms:metE3079::Tn10 nnnThe Tn10 in CAG13491 is inserted in the metE regulatory region, but causes a Met- phenotype.

edit 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:EG10837

EchoBASE (EcoliWiki Page)

EchoBASE:EB0830

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3778

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4698

EcoGene (EcoliWiki Page)

EcoGene:EG10837

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:REP

CGSC (EcoliWiki Page)

CGSC:303

ASAP (EcoliWikiPage)

ASAP:ABE-0012344


edit table


Notes

Links

[back to top]


Name URL Comments
edit table


References

[back to top]


  1. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 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
  4. ↑ Takahashi, S et al. (1979) The rep mutation. VI. Purification and properties of the Escherichia coli rep protein, DNA helicase III. Can. J. Biochem. 57 855-66 PubMed
  5. ↑ Tessman, I et al. (1982) Relative map location of the rep and rho genes of Escherichia coli. J. Bacteriol. 151 1637-40 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 CGSC: The Coli Genetics Stock Center
  8. ↑ 8.0 8.1 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=rep:Gene&oldid=650301"