nirD: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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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|-
!align=left {{table_heading_style}} |Standard name
||
''nirD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''nirD''
Nitrite reductase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3354, b3366, JW3329''<ref name='LIB:Riley_2006'/>, JW3329''


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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.17283.Z46a9f42cb843c&page=17283&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK3354, b3366, JW3329''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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<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="N46a9f42d457a2"  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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75.32 minutes, 75.32 minutes&nbsp;
75.32 minutes, 75.32 minutes&nbsp;
|
|
MG1655: 3494573..3494899<br />{{GBrowseFigureByCoord|3493573|3495899|ecoli|MG1655}}
MG1655: 3494573..3494899<br /><gbrowseImage>
name=NC_000913:3494573..3494899
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10655 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10655 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:3493573..3495899 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|3493573|3495899|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:3494573..3494899&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|3494573|3494899|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10655 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10655 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 3424456..3424782<br /><gbrowseImage>
name=NC_012967:3424456..3424782
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|3424456|3424782|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|3424456|3424782|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 3381730..3382056<br /><gbrowseImage>
name=NC_012759:3381730..3382056
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3381730|3382056|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3381730|3382056|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4143865..4143539<br />{{GBrowseFigureByCoord|4142539|4144865|ecoli_W3110|W3110}}  
W3110: 4143865..4143539<br /><gbrowseImage>
name=NC_007779:4143539..4143865
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|4142539|4144865|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|4143539|4143865|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 3592318..3592644<br /><gbrowseImage>
name=NC_010473:3592318..3592644
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:4142539..4144865 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|3591666|3593296|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4143539..4143865&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|3591666|3593296|FASTA Dump}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9f42e0633f"  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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====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="K46a9f42e4f37f"  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!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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&Delta;nirD (Keio:JW3329)
&Delta;nirD (Keio:JW3329)
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[[PMID:16738554]]<ref name=PMID:16738554/>|[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]   
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=108770 CGSC10489]<ref name='LIB:cgsc'/>
|
   
|-
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''&#916;nirD774::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
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[[cgscmutation:102082|CGSC:102082]]
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<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW3329
JW3329
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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:CCACCGCGCAGCTGCACCACGCC  
Primer 2:CCACCGCGCAGCTGCACCACGCC  
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[[:Category:Kohara_Phage:15C3|15C3]]
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Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=624 Genobase]
|
PMID:3038334
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|
[[smg:Gene|smg-3082::Tn10]]
|
Linked marker
|
CAG12071 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40240 CGSC7444]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 2% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
|-
|
[[yhfT:Gene|zhf-3084::Tn10]]
|
Linked marker
|
CAG18456 = [http://cgsc2.biology.yale.edu/Strain.php?ID=61450 CGSC7576]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 75% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
 
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG10655 EcoCyc:EG10655] 
|
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0649 EchoBASE:EB0649] 
EcoCyc:EG10655
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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]])
[[EcoGene]]
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|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3366 EcoliGenExpDB:b3366] 
EcoGene:EG10655
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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]])
[[RegulonDB]]
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|
[http://BioCyc.org/ECOL199310/new-image?object=C4142 ECOL199310CYC:C4142] 
RegulonDB:ECK120000648
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG10655 EcoGene:EG10655]
[http://www.ncbi.nlm.nih.gov/gene?term=947881 GeneID:947881]
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Escherichia coli str. K-12 substr. MG1655
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=NIRD ECOO157CYC:NIRD] 
EchoBASE:EB0649
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/35425 CGSC:35425] 
ASAP:ABE-0011005
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:nir genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:47, 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

nirD

Mnemonic

Nitrite reductase

Synonyms

ECK3354, b3366, JW3329[1], JW3329

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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

75.32 minutes, 75.32 minutes 

MG1655: 3494573..3494899
<gbrowseImage> name=NC_000913:3494573..3494899 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3424456..3424782
<gbrowseImage> name=NC_012967:3424456..3424782 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3381730..3382056
<gbrowseImage> name=NC_012759:3381730..3382056 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4143865..4143539
<gbrowseImage> name=NC_007779:4143539..4143865 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3592318..3592644
<gbrowseImage> name=NC_010473:3592318..3592644 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

ΔnirD (Keio:JW3329)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10489[3]

ΔnirD774::kan

PMID:16738554[2]

CGSC:102082


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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

JW3329

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAGCCAGTGGAAAGACATCTG

Primer 2:CCACCGCGCAGCTGCACCACGCC

15C3

Kohara Phage

Genobase

PMID:3038334[5]

smg-3082::Tn10

Linked marker

CAG12071 = CGSC7444[3]

est. P1 cotransduction: 2% [6]
Synonyms:zhb-3082::Tn10, zhd-3082::Tn10

zhf-3084::Tn10

Linked marker

CAG18456 = CGSC7576[3]

est. P1 cotransduction: 75% [6]
Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).

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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:EG10655

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10655

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000648

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947881

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0649

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011005

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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