uidB:Gene: Difference between revisions

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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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*  
*  
****************************************************************************************** -->{{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="E46a9cae84c3ab" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''uidB''  
''uidB''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
hexUronIDes
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1611, b1616, JW1608, gusB, uidP''<ref name='LIB:Riley_2006'/>
''ECK1611, b1616, JW1608, gusB, uidP''<ref name='LIB:Riley_2006'/>, uidP''


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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="R46a9cae8c7869"  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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36.44 minutes&nbsp;
36.44 minutes&nbsp;
|
|
MG1655: 1692287..1690914<br />{{GBrowseFigureByCoord|1689914|1693287|ecoli|MG1655}}
MG1655: 1692287..1690914<br /><gbrowseImage>
name=NC_000913:1690914..1692287
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11658 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11658 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1689914|1693287|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1689914|1693287|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|1690914|1692287|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1690914|1692287|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11658 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11658 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 1671458..1670085<br /><gbrowseImage>
name=NC_012967:1670085..1671458
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|1670085|1671458|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|1670085|1671458|FASTA Dump}}
|-  
|-  
|
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&nbsp;
&nbsp;
|
|
W3110: 1695977..1694604<br />{{GBrowseFigureByCoord|1693604|1696977|ecoli_W3110|W3110}}
W3110: 1695977..1694604<br /><gbrowseImage>
name=NC_007779:1694604..1695977
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1693604|1696977|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1693604|1696977|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1694604|1695977|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1694604|1695977|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 1783248..1781875<br /><gbrowseImage>
name=NC_010473:1781875..1783248
source=DH10B
preset=GeneLocation
</gbrowseImage>


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{{GBrowseLink|DH10B|NC_010473|1779129|1785994|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1779129|1785994|FASTA Dump}}
 
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*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_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="W46a9cae97887e"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
1690914
|
Edman degradation
|
PMID:15774881<br />
|


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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}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="N46a9cae9bb845"  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
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|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107650 CGSC9369]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107650 CGSC9369]<ref name='LIB:cgsc'/>  
|
|
   
   
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0005407 uidB::Tn5KAN-2] (FB20390)
|
Insertion at nt 333 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20390]
|
does not contain [[pKD46]]
|-
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?FeatureID=ABE-0005407 uidB::Tn5KAN-2] (FB20391)
|
Insertion at nt 333 in Plus orientation
|
|
|
|
PMID:15262929
|
[http://www.genome.wisc.edu/resources/forms/strainrequest.htm E. coli Genome Project:FB20391]
|
contains [[pKD46]]
|-  
|-  
|
|
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|
|


|[[PMID:16738554]]<ref name=PMID:16738554/>
|
PMID:16738554
|
|
[[cgscmutation:103300|CGSC:103300]]
[[cgscmutation:103300|CGSC:103300]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13797.B4e04c540596c0-->
<!--
******************************************************************************************
*
*  ** 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="B4e04c540596c0"  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.13797.B4e04c540596c0&page=13797&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13797.B4e04c540596c0--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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*  
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****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
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|- {{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:Clone OK
Status:Clone OK
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Primer 2:CCATTAGTGATATCGCTGATTAA  
Primer 2:CCATTAGTGATATCGCTGATTAA  
|-
|
[[:Category:Kohara_Phage:6A5|6A5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=314 Genobase]
|
PMID:3038334
|-  
|-  
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Synonyms:zdh-925::Tn10  
Synonyms:zdh-925::Tn10  


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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="X46a9caeb083db"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11658 EcoCyc:EG11658]
EcoCyc:EG11658
|
|
''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=EB1610 EchoBASE:EB1610]
EcoGene:EG11658
|
|
''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=b1616 EcoliGenExpDB:b1616]
RegulonDB:ECK120001601
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOL199310/new-image?object=C2008 ECOL199310CYC:C2008]
|
|-  
|-  
|
|
[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=EG11658 EcoGene:EG11658]
[http://www.ncbi.nlm.nih.gov/gene?term=947484 GeneID:947484]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=UIDB ECOO157CYC:UIDB]
EchoBASE:EB1610
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0005407&formSubmitReturn=1 ASAP:ABE-0005407]
ASAP:ABE-0005407
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:uid genes]]
[[Category:uid genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]

Latest revision as of 20:28, 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

[back to top]


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

Standard name

uidB

Mnemonic

hexUronIDes

Synonyms

ECK1611, b1616, JW1608, gusB, uidP[1], uidP

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

36.44 minutes 

MG1655: 1692287..1690914
<gbrowseImage> name=NC_000913:1690914..1692287 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1671458..1670085
<gbrowseImage> name=NC_012967:1670085..1671458 source=REL606 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1695977..1694604
<gbrowseImage> name=NC_007779:1694604..1695977 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1783248..1781875
<gbrowseImage> name=NC_010473:1781875..1783248 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


Notes

Sequence Features

[back to top]


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

1690914

Edman degradation

PMID:15774881[2]


edit table


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

ΔuidB (Keio:JW1608)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC9369[4]

uidB::Tn5KAN-2 (FB20390)

Insertion at nt 333 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20390

does not contain pKD46

uidB::Tn5KAN-2 (FB20391)

Insertion at nt 333 in Plus orientation

PMID:15262929[5]

E. coli Genome Project:FB20391

contains pKD46

ΔuidB764::kan

PMID:16738554[3]

CGSC:103300


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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

JW1608

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAATCAACAACTCTCCTGGCG

Primer 2:CCATTAGTGATATCGCTGATTAA

6A5

Kohara Phage

Genobase

PMID:3038334[7]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[4]

est. P1 cotransduction: % [8]
Synonyms:zdc-235::Tn10

zdi-925::Tn10

Linked marker

CAG12151 = CGSC7385[4]

est. P1 cotransduction: % [8]
Synonyms:zdh-925::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:EG11658

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11658

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001601

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947484

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1610

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0005407

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. ↑ Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ Liang, WJ et al. (2005) The gusBC genes of Escherichia coli encode a glucuronide transport system. J. Bacteriol. 187 2377-85 PubMed
  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. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 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. ↑ 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
  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).

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