dppF:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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{|   id="K46a9f87f665ab"  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="K46a9f87f665ab"  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: 3700891..3699887<br /><gbrowseImage>
MG1655: 3700891..3699887<br /><gbrowseImage>
name=NC_000913:3699887..3700891
name=NC_000913:3699887..3700891
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12628 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12628 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3698887|3701891|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3698887|3701891|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3699887|3700891|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3699887|3700891|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12628 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12628 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|3588381|NC_3589385|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|3588381|3589385|GBrowse (BW2952)}}
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W3110: 3937547..3938551<br /><gbrowseImage>
W3110: 3937547..3938551<br /><gbrowseImage>
name=AC_000091:3937547..3938551
name=NC_007779:3937547..3938551
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
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{{GBrowseLink|ecoli_W3110|AC_000091|3936547|3939551|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3936547|3939551|GBrowse(W3110)}}  
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DH10B: 3798636..3797632<br /><gbrowseImage>
DH10B: 3798636..3797632<br /><gbrowseImage>
name=NC_010473:3797632..3798636
name=NC_010473:3797632..3798636
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
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{{GBrowseLink|ecoli_DH10B|NC_010473|3795624|3800644|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|3795624|3800644|GBrowse(DH10B)}}
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{|   id="M46a9f88028caa"  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="M46a9f88028caa"  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="M46a9f88072422"  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="M46a9f88072422"  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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''dppF::Kan''
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Auxotrophies
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Abolished heme utilization.
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PMID:16905647
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Experimental Strain: JWN3509-2
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See table 1. 


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{|   id="G4e04ba11b17c1"  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="G4e04ba11b17c1"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
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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="G46a9f88134596"  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="G46a9f88134596"  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:CCACGCTGCGGATTTTCATCCTG  
Primer 2:CCACGCTGCGGATTTTCATCCTG  
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[[:Category:Kohara_Phage:1D1|1D1]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=603 Genobase]
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PMID:3038334
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{|   id="U46a9f881d1f3d"  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="U46a9f881d1f3d"  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=EG12628 EcoCyc:EG12628]
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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=EB2512 EchoBASE:EB2512]
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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=b3540 EcoliGenExpDB:b3540]
EcoCyc:EG12628
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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=C4355 ECOL199310CYC:C4355]
EcoGene:EG12628
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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=EG12628 EcoGene:EG12628]
RegulonDB:ECK120002340
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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=DPPF ECOO157CYC:DPPF]
[http://www.ncbi.nlm.nih.gov/gene?term=948056 GeneID:948056]
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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/33752 CGSC:33752]
EchoBASE:EB2512
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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=0011564&formSubmitReturn=1 ASAP:ABE-0011564]
ASAP:ABE-0011564
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments
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Latest revision as of 20:48, 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

dppF

Mnemonic

Dipeptide permease system

Synonyms

ECK3527, b3540, JW3509, dppE[1]

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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

79.74 minutes 

MG1655: 3700891..3699887
<gbrowseImage> name=NC_000913:3699887..3700891 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3633326..3632322
<gbrowseImage> name=NC_012967:3632322..3633326 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3588381..3589385
<gbrowseImage> name=NC_012759:3588381..3589385 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3937547..3938551
<gbrowseImage> name=NC_007779:3937547..3938551 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3798636..3797632
<gbrowseImage> name=NC_010473:3797632..3798636 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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
edit table


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

ΔdppF (Keio:JW3509)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10595[3]

dppF::Tn5KAN-I-SceI (FB21266)

Insertion at nt 329 in Plus orientation

PMID:15262929[4]

E. coli Genome Project:FB21266

contains pKD46

ΔdppF723::kan

PMID:16738554[2]

CGSC:100644

dppF::Kan

Auxotrophies

Abolished heme utilization.

PMID:16905647[5]

Experimental Strain: JWN3509-2

See table 1.

edit table


Notes

Genetic Interactions

[back to top]



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

JW3509

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCAGTACGCAAGAGGCCACCCT

Primer 2:CCACGCTGCGGATTTTCATCCTG

1D1

Kohara Phage

Genobase

PMID:3038334[7]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[3]

est. P1 cotransduction: % [8]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[3]

est. P1 cotransduction: % [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:EG12628

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12628

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002340

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948056

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2512

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0011564

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. ↑ Kang, Y et al. (2004) Systematic mutagenesis of the Escherichia coli genome. J. Bacteriol. 186 4921-30 PubMed
  5. ↑ Létoffé, S et al. (2006) The housekeeping dipeptide permease is the Escherichia coli heme transporter and functions with two optional peptide binding proteins. Proc. Natl. Acad. Sci. U.S.A. 103 12891-6 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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