serC:Gene: Difference between revisions

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|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0898, b0907, JW0890, pdxC, pdxF''<ref name='LIB:Riley_2006'/>
''ECK0898, b0907, JW0890, pdxC, pdxF''<ref name='LIB:Riley_2006'/>, pdxF''


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{|   id="T46a9bb61637fb"  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="T46a9bb61637fb"  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: 956876..957964<br /><gbrowseImage>
MG1655: 956876..957964<br /><gbrowseImage>
name=NC_000913:956876..957964
name=NC_000913:956876..957964
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=EG10946 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG10946 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|955876|958964|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|955876|958964|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|956876|957964|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|956876|957964|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10946 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10946 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|859844|NC_860932|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|859844|860932|GBrowse (BW2952)}}
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W3110: 958075..959163<br /><gbrowseImage>
W3110: 958075..959163<br /><gbrowseImage>
name=AC_000091:958075..959163
name=NC_007779:958075..959163
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|957075|960163|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|957075|960163|GBrowse(W3110)}}  
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DH10B: 1010804..1011892<br /><gbrowseImage>
DH10B: 1010804..1011892<br /><gbrowseImage>
name=NC_010473:1010804..1011892
name=NC_010473:1010804..1011892
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_DH10B|NC_010473|1008628|1014068|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1008628|1014068|GBrowse(DH10B)}}
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{|   id="B46a9bb620dbc5"  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="B46a9bb620dbc5"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
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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="Z46a9bb624e319"  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="Z46a9bb624e319"  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!!Comments
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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pdxF5
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Auxotrophies
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Mutation in allele causes production of pyridoxine to halt and can be restored when supplemented with L-serine, Figure 1.
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PMID:4321330
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[http://cgsc.biology.yale.edu/Site.php?ID=171 pdxF]
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Strain History: WG1
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SerC57
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Auxotrophies
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Mutation causes double requirement for pyridoxine and serine due to lack of 3-phosphoserine-2-oxoglutarate aminotransferase (POA), Figure 6.
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PMID:4321330
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Strain History: WG1145


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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.12373.I4e04c3b7232fc-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="I4e04c3b7232fc"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.12373.I4e04c3b7232fc&page=12373&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="C46a9bb62ec597"  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="C46a9bb62ec597"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCACCGTGACGGCGTTCGAACTC  
Primer 2:CCACCGTGACGGCGTTCGAACTC  
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[[:Category:Kohara_Phage:13E3|13E3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=216 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:6D12|6D12]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=217 Genobase]
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PMID:3038334
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{|   id="M46a9bb6382465"  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="M46a9bb6382465"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
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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=EG10946 EcoCyc:EG10946]
EcoCyc:EG10946
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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]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB0939 EchoBASE:EB0939]
EcoGene:EG10946
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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]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0907 EcoliGenExpDB:b0907]
RegulonDB:ECK120000935
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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]])
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[http://BioCyc.org/ECOL199310/new-image?object=C1045 ECOL199310CYC:C1045]
[http://www.ncbi.nlm.nih.gov/gene?term=945527 GeneID:945527]
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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=EG10946 EcoGene:EG10946]
EchoBASE:EB0939
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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=SERC ECOO157CYC:SERC]
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[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
ASAP:ABE-0003093
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[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/171 CGSC:171]
''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]])
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0003093&formSubmitReturn=1 ASAP:ABE-0003093]
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Latest revision as of 20:32, 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

serC

Mnemonic

Serine

Synonyms

ECK0898, b0907, JW0890, pdxC, pdxF[1], pdxF

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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

20.62 minutes 

MG1655: 956876..957964
<gbrowseImage> name=NC_000913:956876..957964 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 974745..975833
<gbrowseImage> name=NC_012967:974745..975833 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 859844..860932
<gbrowseImage> name=NC_012759:859844..860932 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 958075..959163
<gbrowseImage> name=NC_007779:958075..959163 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1010804..1011892
<gbrowseImage> name=NC_010473:1010804..1011892 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

Coding Start (SO:0000323)

MG1655

956879

Edman degradation

PMID:9298646[2]
PMID:9740056[3]


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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

ΔserC (Keio:JW0890)

deletion

deletion

PMID:16738554[4]

Shigen
CGSC8913[5]

serC53

CGSC:9696

serC13

CGSC:10177

serC903

CGSC:23663

ΔserC731::kan

PMID:16738554[4]

CGSC:102918

pdxF5

Auxotrophies

Mutation in allele causes production of pyridoxine to halt and can be restored when supplemented with L-serine, Figure 1.

PMID:4321330[6]

pdxF

Strain History: WG1

SerC57

Auxotrophies

Mutation causes double requirement for pyridoxine and serine due to lack of 3-phosphoserine-2-oxoglutarate aminotransferase (POA), Figure 6.

PMID:4321330[6]

Strain History: WG1145

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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

JW0890

Plasmid clone

Shigen

PMID:16769691[7]

Status:Clone OK

Primer 1:GCCGCTCAAATCTTCAATTTTAG

Primer 2:CCACCGTGACGGCGTTCGAACTC

13E3

Kohara Phage

Genobase

PMID:3038334[8]

6D12

Kohara Phage

Genobase

PMID:3038334[8]

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[5]

est. P1 cotransduction: 70% [9]
Synonyms:zbj-1230::Tn10

zcb-3059::Tn10

Linked marker

CAG12094 = CGSC7358[5]

est. P1 cotransduction: 13% [9]

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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:EG10946

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG10946

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120000935

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945527

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB0939

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0003093

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. ↑ Link, AJ et al. (1997) Comparing the predicted and observed properties of proteins encoded in the genome of Escherichia coli K-12. Electrophoresis 18 1259-313 PubMed
  3. ↑ Tonella, L et al. (1998) '98 Escherichia coli SWISS-2DPAGE database update. Electrophoresis 19 1960-71 PubMed
  4. ↑ 4.0 4.1 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
  5. ↑ 5.0 5.1 5.2 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 Dempsey, WB & Ito, H (1970) Characterization of pyridoxine auxotrophs of Escherichia coli: serine and pdxF mutants. J. Bacteriol. 104 658-67 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 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).

Categories

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