bcp:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|bcp}}{{Tab On|Gene|bcp}}{{Tab|Gene Product(s)|bcp}}{{Tab|Expression|bcp}}{{Tab|Evolution|bcp}}{{Tab|On One Page|bcp}}{{TabsBottom}}
{{Tab|Quickview|bcp}}{{Tab On|Gene|bcp}}{{Tab|Gene Product(s)|bcp}}{{Tab|Expression|bcp}}{{Tab|Evolution|bcp}}{{Tab|On One Page|bcp}}{{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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</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''bcp''  
''bcp''
|-
!align=left {{table_heading_style}} |Mnemonic
||
Bacterioferritin comigratory protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2476, b2480, JW2465''<ref name='LIB:Riley_2006'/>, JW2465''


|-
|- class="tableEdit_footer"
!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15527.V46a9df03391d8&page=15527&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2476, b2480, JW2465''<ref name='LIB:Riley_2006'/>
|-
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{{Gene_nomenclature_help}}
 
<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===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="E46a9df03b6ba6"  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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MG1655
MG1655
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56.01 minutes&nbsp;
56.01 minutes&nbsp;
|
|
MG1655: 2598500..2598970<br />{{GBrowseFigureByCoord|2597500|2599970|ecoli|MG1655}}
MG1655: 2598500..2598970<br /><gbrowseImage>
name=NC_000913:2598500..2598970
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10108 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10108 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2597500..2599970 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2597500|2599970|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2598500..2598970&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2598500|2598970|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10108 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10108 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 2521306..2521776<br /><gbrowseImage>
name=NC_012967:2521306..2521776
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2521306|2521776|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|2521306|2521776|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 2484305..2484775<br /><gbrowseImage>
name=NC_012759:2484305..2484775
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2484305|2484775|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|2484305|2484775|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
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W3110: 2599134..2599604<br />{{GBrowseFigureByCoord|2598134|2600604|ecoli_W3110|W3110}}
W3110: 2599134..2599604<br /><gbrowseImage>
name=NC_007779:2599134..2599604
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2598134..2600604 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|2598134|2600604|GBrowse(W3110)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2599134..2599604&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|2599134|2599604|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 2690265..2690735<br /><gbrowseImage>
name=NC_010473:2690265..2690735
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|2689325|2691675|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|2689325|2691675|FASTA Dump}}
 
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<!--Location_notes--></protect>
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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="G46a9df046f675"  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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Coding Start (SO:0000323)
|
[[MG1655]]
|
2598500
|
Edman degradation
|
PMID:9298646<br />PMID:9740056<br />
|
 
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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="J46a9df04b5214"  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
|-
|-
|
&Delta;bcp (Keio:JW2465)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108247 CGSC9966]<ref name='LIB:cgsc'/>
|
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0008171 bcp::Tn5KAN-2] (FB20824)
|
Insertion at nt 281 in Plus orientation
|
 
|
 
|
 
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20824]
|
contains [[pKD46]]
|-
|
''&#916;bcp-728::kan''
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
 
|
|
&nbsp;
PMID:16738554
|
|
&nbsp;
[[cgscmutation:100158|CGSC:100158]]
|
|
&nbsp;
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15527.W4e04b81d04b34-->
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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|- {{table_heading_style}}
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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|
JW2465
JW2465
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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:Clone OK
Status:Clone OK
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Primer 2:CCGGCGTGTTCTTTCAGCCAGTT  
Primer 2:CCGGCGTGTTCTTTCAGCCAGTT  
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[[:Category:Kohara_Phage:4C11|4C11]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=423 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5A8|5A8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=424 Genobase]
|
PMID:3038334
|-
|
[[purC:Gene|purC80::Tn10]]
|
Linked marker
|
CAG18470 = [http://cgsc2.biology.yale.edu/Strain.php?ID=38904 CGSC7413]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 85% <ref name='LIB:Nichols_linked_Tn'/>
|-
|
[[hcaT:Gene|zfh-208::Tn10]]
|
Linked marker
|
CAG18481 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40086 CGSC7417]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 3% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zff-208::Tn10
 
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<protect><!--Gene_resources_notes--></protect>
<protect><!--Gene_resources_notes--></protect>
===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10108 EcoCyc:EG10108] 
EcoCyc:EG10108
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0106 EchoBASE:EB0106] 
EcoGene:EG10108
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2480 EcoliGenExpDB:b2480] 
RegulonDB:ECK120000104
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C3008 ECOL199310CYC:C3008]
[http://www.ncbi.nlm.nih.gov/gene?term=946949 GeneID:946949]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10108 EcoGene:EG10108] 
EchoBASE:EB0106
|
|
''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=BCP ECOO157CYC:BCP] 
ASAP:ABE-0008171
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-
 
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15527.O46a9df06129b1&page=15527&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/33035 CGSC:33035] 
|
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==Links==
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__NOTOC__
__NOTOC__
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]</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:bcp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:42, 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

bcp

Mnemonic

Bacterioferritin comigratory protein

Synonyms

ECK2476, b2480, JW2465[1], JW2465

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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

56.01 minutes 

MG1655: 2598500..2598970
<gbrowseImage> name=NC_000913:2598500..2598970 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2521306..2521776
<gbrowseImage> name=NC_012967:2521306..2521776 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2484305..2484775
<gbrowseImage> name=NC_012759:2484305..2484775 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2599134..2599604
<gbrowseImage> name=NC_007779:2599134..2599604 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2690265..2690735
<gbrowseImage> name=NC_010473:2690265..2690735 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

Coding Start (SO:0000323)

MG1655

2598500

Edman degradation

PMID:9298646[2]
PMID:9740056[3]


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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

Δbcp (Keio:JW2465)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC9966[5]

bcp::Tn5KAN-2 (FB20824)

Insertion at nt 281 in Plus orientation

PMID:15262929[6]

E. coli Genome Project:FB20824

contains pKD46

Δbcp-728::kan

PMID:16738554[4]

CGSC:100158


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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

JW2465

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCAATCCACTGAAAGCCGGTGA

Primer 2:CCGGCGTGTTCTTTCAGCCAGTT

4C11

Kohara Phage

Genobase

PMID:3038334[8]

5A8

Kohara Phage

Genobase

PMID:3038334[8]

purC80::Tn10

Linked marker

CAG18470 = CGSC7413[5]

est. P1 cotransduction: 85% [9]

zfh-208::Tn10

Linked marker

CAG18481 = CGSC7417[5]

est. P1 cotransduction: 3% [9]
Synonyms:zff-208::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:EG10108

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10108

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000104

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946949

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0106

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0008171

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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<protect>

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  7. ↑ 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
  8. ↑ 8.0 8.1 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
  9. ↑ 9.0 9.1 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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