ais: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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{|{{Prettytable}}
{|   id="B46a9d9a28c983"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ais''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ais''
Aluminum inducible
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK2245, b2252, JW2246''<ref name='LIB:Riley_2006'/>, JW2246, pagH, pmrG''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.15065.B46a9d9a28c983&page=15065&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK2245, b2252, JW2246''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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|- {{table_heading_style}}
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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
MG1655
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50.93 minutes&nbsp;
50.93 minutes&nbsp;
|
|
MG1655: 2363642..2363040<br />{{GBrowseFigureByCoord|2362040|2364642|ecoli|MG1655}}
MG1655: 2363642..2363040<br /><gbrowseImage>
name=NC_000913:2363040..2363642
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7165 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7165 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:2362040..2364642 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|2362040|2364642|GBrowse(MG1655)}}
   
   
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:2363040..2363642&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|2363040|2363642|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7165 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7165 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 2312133..2311531<br /><gbrowseImage>
name=NC_012967:2311531..2312133
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|2311531|2312133|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|2311531|2312133|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 2248845..2249447<br /><gbrowseImage>
name=NC_012759:2248845..2249447
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|2248845|2249447|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|2248845|2249447|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 2370290..2369688<br />{{GBrowseFigureByCoord|2368688|2371290|ecoli_W3110|W3110}}  
W3110: 2370290..2369688<br /><gbrowseImage>
name=NC_007779:2369688..2370290
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|2368688|2371290|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|2369688|2370290|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 2454630..2454028<br /><gbrowseImage>
name=NC_010473:2454028..2454630
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:2368688..2371290 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|2452824|2455834|GBrowse(DH10B)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:2369688..2370290&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|2452824|2455834|FASTA Dump}}
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===Notes===
===Notes===
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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{|class = 'sortable' {{Prettytable}} id='138393'
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!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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&Delta;ais (Keio:JW2246)
&Delta;ais (Keio:JW2246)
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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=108092 CGSC9811]<ref name='LIB:cgsc'/>  
|
|-
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''&#916;ais-733::kan''
|
 
|
 
|
 
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108092 CGSC9811]<ref name='LIB:cgsc'/> 
 
|
PMID:16738554
|
[[cgscmutation:99958|CGSC:99958]]
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.15065.R4e04b71c490e1-->
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW2246
JW2246
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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]
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCGTGGTTAACGAATTCCCCATC  
Primer 2:CCGTGGTTAACGAATTCCCCATC  
|-
|-
|
[[:Category:Kohara_Phage:4B4|4B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=379 Genobase]
|
PMID:3038334
|-  
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[[yfaL:Gene|zfa-723::Tn10]]
[[yfaL:Gene|zfa-723::Tn10]]
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CAG12178 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44155 CGSC7526]<ref name='LIB:cgsc'/>
CAG12178 gyrA+ = [http://cgsc2.biology.yale.edu/Strain.php?ID=44155 CGSC7526]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 48% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 48% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).  
Synonyms:zei-723::Tn10, zfa-723::Tn10  
|-  
 
 
The original CAG12178 was NalR.  This is a NalS derivative constructed by S. McAteer (CGSC).  
|-
|
|
[[yfbO:Gene|zfb-223::Tn10]]
[[yfbO:Gene|zfb-223::Tn10]]
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CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
CAG18484 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40073 CGSC7406]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 37% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 37% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zej-223::Tn10


Synonyms:zej-223::Tn10
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!Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7165 EcoCyc:G7165] 
EcoCyc:G7165
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|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2949 EchoBASE:EB2949] 
EcoGene:EG13155
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b2252 EcoliGenExpDB:b2252] 
RegulonDB:ECK120003741
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2794 ECOL199310CYC:C2794]
[http://www.ncbi.nlm.nih.gov/gene?term=944945 GeneID:944945]
|
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Escherichia coli str. K-12 substr. MG1655
|-
|-  
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
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[http://ecogene.org/geneinfo.php?eg_id=EG13155 EcoGene:EG13155] 
EchoBASE:EB2949
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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]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=AIS ECOO157CYC:AIS] 
ASAP:ABE-0007451
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===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:ais genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:41, 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

ais

Mnemonic

Aluminum inducible

Synonyms

ECK2245, b2252, JW2246[1], JW2246, pagH, pmrG

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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

50.93 minutes 

MG1655: 2363642..2363040
<gbrowseImage> name=NC_000913:2363040..2363642 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2312133..2311531
<gbrowseImage> name=NC_012967:2311531..2312133 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2248845..2249447
<gbrowseImage> name=NC_012759:2248845..2249447 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2370290..2369688
<gbrowseImage> name=NC_007779:2369688..2370290 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2454630..2454028
<gbrowseImage> name=NC_010473:2454028..2454630 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

Δais (Keio:JW2246)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9811[3]

Δais-733::kan

PMID:16738554[2]

CGSC:99958


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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

JW2246

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTTAGCTTTTTGCCGCTCTTC

Primer 2:CCGTGGTTAACGAATTCCCCATC

4B4

Kohara Phage

Genobase

PMID:3038334[5]

zfa-723::Tn10

Linked marker

CAG12178 gyrA+ = CGSC7526[3]

est. P1 cotransduction: 48% [6]
Synonyms:zei-723::Tn10, zfa-723::Tn10 nnnThe original CAG12178 was NalR. This is a NalS derivative constructed by S. McAteer (CGSC).

zfb-223::Tn10

Linked marker

CAG18484 = CGSC7406[3]

est. P1 cotransduction: 37% [6]
Synonyms:zej-223::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:G7165

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13155

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003741

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944945

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2949

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0007451

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. ↑ 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. ↑ 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
  5. ↑ 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
  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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