dinB:Gene: Difference between revisions

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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>
''ECK0232, b0231, JW0221, dinP''<ref name='LIB:Riley_2006'/>, dinP''


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{|   id="O46a9ab5b8e4d7"  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="O46a9ab5b8e4d7"  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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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6115 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6115 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|249898|252953|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|249898|252953|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|250898|251953|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|250898|251953|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6115 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6115 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|250897|NC_251952|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|250897|251952|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|250897|NC_251952|FASTA Dump}}  
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W3110: 250898..251953<br /><gbrowseImage>
W3110: 250898..251953<br /><gbrowseImage>
name=AC_000091:250898..251953
name=NC_007779:250898..251953
source=MG1655_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|249898|252953|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|249898|252953|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|250898|251953|FASTA Dump}}  
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DH10B: 225002..226057<br /><gbrowseImage>
DH10B: 225002..226057<br /><gbrowseImage>
name=NC_010473:225002..226057
name=NC_010473:225002..226057
source=MG1655_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|222892|228167|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|222892|228167|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|222892|228167|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|222892|228167|FASTA Dump}}  


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{|   id="M46a9ab5c383cc"  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="M46a9ab5c383cc"  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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{| {{Prettytable}} id="S46a9ab5c79313"  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="S46a9ab5c79313"  class=" tableEdit Gene_allele_table dataTable"   
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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;dinB (Keio:JW0221)
''dinB(del)'' (Keio:JW0221)
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deletion
deletion
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PMID:16738554
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106737 CGSC8456]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
 
[http://cgsc2.biology.yale.edu/Strain.php?ID=106737 CGSC8456]<ref name='LIB:cgsc'/>  
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Other
 
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xx
xx
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F172A
F172A
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''&#916;dinB749::kan''
''dinB749(del)::kan''
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{|   id="G4e04b9d83d5b6"  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="G4e04b9d83d5b6"  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="N46a9ab5d22bd7"  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="N46a9ab5d22bd7"  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:CCTAATCCCAGCACCAGTTGTCT  
Primer 2:CCTAATCCCAGCACCAGTTGTCT  
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[[:Category:Kohara_Phage:8F9|8F9]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=127 Genobase]
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PMID:3038334
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{|   id="V46a9ab5dacd15"  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="V46a9ab5dacd15"  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=G6115 EcoCyc:G6115]
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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=EB2935 EchoBASE:EB2935]
EcoCyc:G6115
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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=b0231 EcoliGenExpDB:b0231]
EcoGene:EG13141
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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=C0379 ECOL199310CYC:C0379]
RegulonDB:ECK120002735
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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]])
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[http://ecogene.org/geneinfo.php?eg_id=EG13141 EcoGene:EG13141]
[http://www.ncbi.nlm.nih.gov/gene?term=944922 GeneID:944922]
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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=DINP ECOO157CYC:DINP]
EchoBASE:EB2935
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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=0000789&formSubmitReturn=1 ASAP:ABE-0000789]
ASAP:ABE-0000789
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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 20:37, 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

dinB

Mnemonic

damage inducible Damage inducible

Synonyms

ECK0232, b0231, JW0221, dinP[1], dinP

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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

5.41 minutes 

MG1655: 250898..251953
<gbrowseImage> name=NC_000913:250898..251953 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 255461..256516
<gbrowseImage> name=NC_012967:255461..256516 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 250897..251952
<gbrowseImage> name=NC_012759:250897..251952 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 250898..251953
<gbrowseImage> name=NC_007779:250898..251953 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 225002..226057
<gbrowseImage> name=NC_010473:225002..226057 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

dinB(del) (Keio:JW0221)

deletion

deletion

PMID:16738554[2]

Shigen

CGSC8456[3]

dinP::Tn5KAN-I-SceI (FB20062)

Insertion at nt 89 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20062

does not contain pKD46

dinP::Tn5KAN-I-SceI (FB20063)

Insertion at nt 89 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB20063

contains pKD46

dinBA310S

A310S

(in strain: ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2)

Strain variation; seeded from UniProt:Q47155

dinBD321N

D321N

(in strain: ECOR 35D)

Strain variation; seeded from UniProt:Q47155

dinBD8A,H

D8A,H

Loss of function

seeded from UniProt:Q47155

dinBR49A,F

R49A,F

Loss of function

seeded from UniProt:Q47155

dinBD103A,N

D103A,N

Loss of function

seeded from UniProt:Q47155

dinBE104A

E104A

Loss of function

seeded from UniProt:Q47155

dinBM210I

M210I

(in strain: ECOR 37UG, ECOR 45B1, ECOR 51B2, ECOR 52B2, ECOR 58B1 and ECOR 70B1)

Strain variation; seeded from UniProt:Q47155

dinBM210T

M210T

(in strain: ECOR 35D, ECOR 46D, ECOR 49D, ECOR 50D, ECOR 57B2, ECOR 59B2, ECOR 60B2 and ECOR 62B2)

Strain variation; seeded from UniProt:Q47155

dinBR225C

R225C

(in strain: ECOR 59B2 and ECOR 60B2)

Strain variation; seeded from UniProt:Q47155

dinBERR36ARG

ERR36ARG

(in strain: ECOR 45B1)

Strain variation; seeded from UniProt:Q47155

dinBQ124K

Q124K

(in strain: ECOR 35D)

Strain variation; seeded from UniProt:Q47155

dinBN132S

N132S

(in strain: ECOR 34B1 and ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBQ135H

Q135H

(in strain: ECOR 70B1)

Strain variation; seeded from UniProt:Q47155

dinBP170S

P170S

(in strain: ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBA171T

A171T

(in strain: ECOR 45B1, ECOR 46D, ECOR 49D and ECOR 50D)

Strain variation; seeded from UniProt:Q47155

dinBL176F

L176F

(in strain: ECOR 37UG)

Strain variation; seeded from UniProt:Q47155

dinBG201S

G201S

(in strain: ECOR 59B2)

Strain variation; seeded from UniProt:Q47155

dinB10

xx

PMID:| SMR

we like this mutation a lot

F172A

PMID:18158902[5]

defective in UMuD interaction

dinB749(del)::kan

PMID:16738554[2]

CGSC:100600


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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

JW0221

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCCGTAAAATCATTCATGTGGA

Primer 2:CCTAATCCCAGCACCAGTTGTCT

8F9

Kohara Phage

Genobase

PMID:3038334[7]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 50% [8]
Synonyms:zae-502::Tn10

proA81::Tn10

Linked marker

CAG18447 = CGSC7330[3]

est. P1 cotransduction: 74% [8]

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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:G6115

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13141

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002735

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944922

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2935

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0000789

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

[back to top]



<protect>

References

[back to top]


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 Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Godoy, VG et al. (2007) UmuD and RecA directly modulate the mutagenic potential of the Y family DNA polymerase DinB. Mol. Cell 28 1058-70 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).

Categories

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