rssB:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL''<ref name='LIB:Riley_2006'/>
''ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL''<ref name='LIB:Riley_2006'/>, verA, ychL''


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{|   id="S46a9c2a5096ce"  class=" tableEdit Gene_location_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="S46a9c2a5096ce"  class=" tableEdit Gene_location_table"   
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!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655: 1289465..1290478<br /><gbrowseImage>
MG1655: 1289465..1290478<br /><gbrowseImage>
name=NC_000913:1289465..1290478
name=NC_000913:1289465..1290478
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12121 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12121 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1288465|1291478|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1288465|1291478|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|1289465|1290478|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1289465|1290478|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12121 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12121 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|1179050|NC_1179976|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1179050|1179976|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|1179050|NC_1179976|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|1179050|1179976|FASTA Dump}}  
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W3110: 1291819..1292832<br /><gbrowseImage>
W3110: 1291819..1292832<br /><gbrowseImage>
name=AC_000091:1291819..1292832
name=NC_007779:1291819..1292832
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|1290819|1293832|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1290819|1293832|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1291819|1292832|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1291819|1292832|FASTA Dump}}  
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DH10B: 1329706..1330719<br /><gbrowseImage>
DH10B: 1329706..1330719<br /><gbrowseImage>
name=NC_010473:1329706..1330719
name=NC_010473:1329706..1330719
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|1327680|1332745|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1327680|1332745|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1327680|1332745|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1327680|1332745|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="L46a9c2a5aac55"  class=" tableEdit Gene_sequence_features_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L46a9c2a5aac55"  class=" tableEdit Gene_sequence_features_table"   
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!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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****************************************************************************************** -->{{Gene_alleles_help}}
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{| {{Prettytable}} id="W46a9c2a5ec566"  class=" tableEdit Gene_allele_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="W46a9c2a5ec566"  class=" tableEdit Gene_allele_table dataTable"   
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|- {{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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Suppressed by pcnA and hfq mutants PMID:19767441  
Suppressed by pcnA and hfq mutants PMID:19767441  
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CAG45114 ''rssB''::Tet
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insertion
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Sigma<sup>E</sup> activity
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Increase in sigma<sup>E</sup> activity
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PMID:23224554
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Paternal Strain: CAG45114
Experimental Strain: SMR15271
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See table S11 for full experimental data. 


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{|   id="L4e04c3508af4c"  class=" tableEdit Genetic_interaction_table dataTable"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="L4e04c3508af4c"  class=" tableEdit Genetic_interaction_table dataTable"   
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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{|   id="U46a9c2a699aad"  class=" tableEdit Gene_resource_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9c2a699aad"  class=" tableEdit Gene_resource_table"   
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCTTCTGCAGACAACATCAAGCG  
Primer 2:CCTTCTGCAGACAACATCAAGCG  
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[[:Category:Kohara_Phage:12H9|12H9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=249 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:4D8|4D8]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=250 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:3D5|3D5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=251 Genobase]
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PMID:3038334
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{|   id="O46a9c2a731f79"  class=" tableEdit Gene_accessions_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a9c2a731f79"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12121 EcoCyc:EG12121]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2042 EchoBASE:EB2042]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1235 EcoliGenExpDB:b1235]
EcoCyc:EG12121
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[EcoGene]]
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[http://BioCyc.org/ECOL199310/new-image?object=C1699 ECOL199310CYC:C1699]
EcoGene:EG12121
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[RegulonDB]]
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[http://ecogene.org/geneinfo.php?eg_id=EG12121 EcoGene:EG12121]
RegulonDB:ECK120002024
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://BioCyc.org/ECOO157/new-image?object=HNR ECOO157CYC:HNR]
[http://www.ncbi.nlm.nih.gov/gene?term=945855 GeneID:945855]
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Escherichia coli str. K-12 substr. MG1655
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[EchoBASE]]
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/37471 CGSC:37471]
EchoBASE:EB2042
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004147&formSubmitReturn=1 ASAP:ABE-0004147]
ASAP:ABE-0004147
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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

Latest revision as of 20:30, 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

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

Standard name

rssB

Mnemonic

Regulation of Sigma S

Synonyms

ECK1230, b1235, JW1223, hnr, mviA, sprE, ychI, ychL[1], verA, ychL

edit table


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

27.79 minutes 

MG1655: 1289465..1290478
<gbrowseImage> name=NC_000913:1289465..1290478 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1290036..1291049
<gbrowseImage> name=NC_012967:1290036..1291049 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1179050..1179976
<gbrowseImage> name=NC_012759:1179050..1179976 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1291819..1292832
<gbrowseImage> name=NC_007779:1291819..1292832 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1329706..1330719
<gbrowseImage> name=NC_010473:1329706..1330719 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
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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

ΔrssB (Keio:JW1223)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9109[3]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire D-Galactoniate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Hydroxybutyrate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Ketobutyrate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire a-Ketoglutarate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Succinate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire Bromosuccinate

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire L-Alanine

PMID:16095938[4]

ΔsprE::kan

deletion

Biolog:respiration

unable to respire L-Asparagine

PMID:16095938[4]

ΔrssB1273

CGSC:77156

ΔrssB744::kan

PMID:16738554[2]

CGSC:102826

overproduction

Growth Phenotype

toxic

Suppressed by pcnA and hfq mutants PMID:19767441[5]

CAG45114 rssB::Tet

insertion

SigmaE activity

Increase in sigmaE activity

PMID:23224554[6]

Paternal Strain: CAG45114 Experimental Strain: SMR15271

See table S11 for full experimental data.

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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

[back to top]


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

Resource Resource Type Source Notes/Reference

JW1223

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCACGCAGCCATTGGTCGGAAA

Primer 2:CCTTCTGCAGACAACATCAAGCG

12H9

Kohara Phage

Genobase

PMID:3038334[8]

4D8

Kohara Phage

Genobase

PMID:3038334[8]

3D5

Kohara Phage

Genobase

PMID:3038334[8]

fadR13::Tn10

Linked marker

CAG18497 = CGSC7365[3]

est. P1 cotransduction: 7% [9]

oppC506::Tn10

Linked marker

CAG12169 = CGSC7369[3]

est. P1 cotransduction: 61% [9]
Synonyms:zch-506::Tn10, zci-506::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:EG12121

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12121

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002024

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945855

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2042

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004147

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. ↑ 2.0 2.1 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
  3. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 4.2 4.3 4.4 4.5 4.6 4.7 4.8 Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ Carabetta, VJ et al. (2009) The response regulator SprE (RssB) modulates polyadenylation and mRNA stability in Escherichia coli. J. Bacteriol. 191 6812-21 PubMed
  6. ↑ Al Mamun, AA et al. (2012) Identity and function of a large gene network underlying mutagenic repair of DNA breaks. Science 338 1344-8 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 8.2 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).

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