gapC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|gapC_1}}{{Tab On|Gene|gapC_1}}{{Tab|Gene Product(s)|gapC_1}}{{Tab|Expression|gapC_1}}{{Tab|Evolution|gapC_1}}{{Tab|On One Page|gapC_1}}{{TabsBottom}}
{{Tab|Quickview|gapC}}{{Tab On|Gene|gapC}}{{Tab|Gene Product(s)|gapC}}{{Tab|Expression|gapC}}{{Tab|Evolution|gapC}}{{Tab|On One Page|gapC}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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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****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="A46a9c68431a31" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''gapC_1''  
''gapC''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''gapC, ECK1409, b1416, JW1413, b1417, JW5906, b4493, JW5906+JW1413, gapC_2''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/><ref name='LIB:EcoCyc10.6'/>
''Note that this is a pseudogene in K12 strains., ECK1409, JW1413, JW5906, b4493''


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9c684b7951"  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
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32.07 minutes&nbsp;
32.07 minutes&nbsp;
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MG1655: 1487988..1487737<br />{{GBrowseFigureByCoord|1486737|1488988|ecoli|MG1655}}
MG1655: 1487988..1487737<br /><gbrowseImage>
name=NC_000913:1487737..1487988
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
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&nbsp;
&nbsp;
|
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W3110: 1491678..1491427<br />{{GBrowseFigureByCoord|1490427|1492678|ecoli_W3110|W3110}}
W3110: 1491678..1491427<br /><gbrowseImage>
name=NC_007779:1491427..1491678
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1490427|1492678|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|1490427|1492678|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1491427|1491678|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|NC_007779|1491427|1491678|FASTA Dump}}  
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32.07 minutes&nbsp;
32.07 minutes&nbsp;
|
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MG1655: 1488737..1487985<br />{{GBrowseFigureByCoord|1486985|1489737|ecoli|MG1655}}
MG1655: 1488737..1487985<br /><gbrowseImage>
name=NC_000913:1487985..1488737
source=ecoli
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1486985..1489737 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|1486985|1489737|GBrowse (MG1655)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1487985..1488737&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|ecoli|NC_000913|1487985|1488737|FASTA Dump}}<br \>
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]
|-  
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&nbsp;
&nbsp;
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W3110: 1492427..1491675<br />{{GBrowseFigureByCoord|1490675|1493427|ecoli_W3110|W3110}}
W3110: 1492427..1491675<br /><gbrowseImage>
name=NC_007779:1491675..1492427
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1490675..1493427 GBrowse(W3110)]
{{GBrowseLink|ecoli_W3110|NC_007779|1490675|1493427|GBrowse (W3110)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1491675..1492427&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|ecoli_W3110|NC_007779|1491675|1492427|FASTA Dump}}<br \>
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
MG1655: 1488737..1487737<br />{{GBrowseFigureByCoord|1486737|1489737|ecoli|MG1655}}
MG1655: 1488737..1487737<br /><gbrowseImage>
name=NC_000913:1487737..1488737
source=ecoli
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G8205 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1486737..1489737 GBrowse(MG1655)]
{{GBrowseLink|ecoli|NC_000913|1486737|1489737|GBrowse (MG1655)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1487737..1488737&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|ecoli|NC_000913|1487737|1488737|FASTA Dump}}<br \>
*[http://biocyc.org/ECOLI/sequence?object=G8205 EcoCyc Sequence Dump]
|-  
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&nbsp;
&nbsp;
|
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W3110: 1492427..1491427<br />{{GBrowseFigureByCoord|1490427|1493427|ecoli_W3110|W3110}}
W3110: 1492427..1491427<br /><gbrowseImage>
name=NC_007779:1491427..1492427
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1490427..1493427 GBrowse(W3110)]
{{GBrowseLink|ecoli_W3110|NC_007779|1490427|1493427|GBrowse (W3110)}}<br \>
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1491427..1492427&plugin_action=Go FASTA Dump]
*{{GBrowseFastaLink|ecoli_W3110|NC_007779|1491427|1492427|FASTA Dump}}<br \>


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="E46a9c6875ce6c" class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{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}}
{| {{Prettytable}}  id="K46a9c6879f08c" class=" tableEdit Gene_allele_table dataTable"
|- {{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
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004727 gapC_2::Tn5KAN-2] (FB20315)
|
Insertion at nt 128 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20314]
|
contains [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0004727 gapC_2::Tn5KAN-2] (FB20315)
|
Insertion at nt 128 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20315]
|
does not contain [[pKD46]]
|-  
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|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[[cgscmutation:101092|CGSC:101092]]
[[cgscmutation:101092|CGSC:101092]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13395.G4e04bbdb1aaae-->
<!--
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*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G4e04bbdb1aaae"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.13395.G4e04bbdb1aaae&page=13395&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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****************************************************************************************** -->{{Gene_resources_help}}
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="D46a9c6884ddf5" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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:3C9|3C9]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=269 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:24D6|24D6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=270 Genobase]
|
PMID:3038334
|-  
|-  
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est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 82% <ref name='LIB:Nichols_linked_Tn'/>  


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*  
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="H46a9c688db690"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G8205 EcoCyc:G8205]
[http://chase.ou.edu/macro/searchlink.php?bnum=b1417 EcoliGenExpDB:b1417]
|
|
   
   
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1417 EcoliGenExpDB:b1417]
[http://BioCyc.org/ECOO157/new-image?object=GAPC ECOO157CYC:GAPC]
|
|
   
   
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12103 EcoGene:EG12103]
[http://www.ncbi.nlm.nih.gov/gene?term=2847738 GeneID:2847738]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=GAPC ECOO157CYC:GAPC]
RegulonDB:ECK120004456
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[EchoBASE]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004727&formSubmitReturn=1 ASAP:ABE-0004727]
EchoBASE:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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==References==
==References==
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes not in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:gap 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

gapC

Mnemonic
Synonyms

Note that this is a pseudogene in K12 strains., ECK1409, JW1413, JW5906, b4493

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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

32.07 minutes 

MG1655: 1487988..1487737
<gbrowseImage> name=NC_000913:1487737..1487988 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1491678..1491427
<gbrowseImage> name=NC_007779:1491427..1491678 source=W3110 preset=GeneLocation </gbrowseImage>

MG1655

32.07 minutes 

MG1655: 1488737..1487985
<gbrowseImage> name=NC_000913:1487985..1488737 source=ecoli preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1492427..1491675
<gbrowseImage> name=NC_007779:1491675..1492427 source=W3110 preset=GeneLocation </gbrowseImage>

MG1655

 

MG1655: 1488737..1487737
<gbrowseImage> name=NC_000913:1487737..1488737 source=ecoli preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1492427..1491427
<gbrowseImage> name=NC_007779:1491427..1492427 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

gapC_2::Tn5KAN-2 (FB20315)

Insertion at nt 128 in Plus orientation

PMID:15262929[1]

E. coli Genome Project:FB20314

contains pKD46

gapC_2::Tn5KAN-2 (FB20315)

Insertion at nt 128 in Plus orientation

PMID:15262929[1]

E. coli Genome Project:FB20315

does not contain pKD46

ΔgapC777::kan

PMID:16738554[2]

CGSC:101092


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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:

3C9

Kohara Phage

Genobase

PMID:3038334[4]

24D6

Kohara Phage

Genobase

PMID:3038334[4]

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[5]

est. P1 cotransduction: 7% [6]

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[5]

est. P1 cotransduction: 82% [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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1417

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:GAPC

NCBI (EcoliWiki Page)

GeneID:2847738

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004456

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

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. ↑ 1.0 1.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  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 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).

Categories

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