mlaC:Gene: Difference between revisions

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Adding section & Genetic interactions table to Gene pages.
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!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK3181, b3192, JW3159'', yrbC<ref name='LIB:Riley_2006'/>
''ECK3181, b3192, JW3159'', yrbC<ref name='LIB:Riley_2006'/>, JW3159, yrbC''


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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="O46a9efda39700"  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="O46a9efda39700"  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: 3335913..3335278<br /><gbrowseImage>
MG1655: 3335913..3335278<br /><gbrowseImage>
name=NC_000913:3335278..3335913
name=NC_000913:3335278..3335913
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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W3110: 3337746..3337111<br /><gbrowseImage>
W3110: 3337746..3337111<br /><gbrowseImage>
name=AC_000091:3337111..3337746
name=NC_007779:3337111..3337746
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3336111|3338746|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|3336111|3338746|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3337111|3337746|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_W3110|NC_007779|3337111|3337746|FASTA Dump}}  
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DH10B: 3433658..3433023<br /><gbrowseImage>
DH10B: 3433658..3433023<br /><gbrowseImage>
name=NC_010473:3433023..3433658
name=NC_010473:3433023..3433658
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="U46a9efdb4159c"  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="U46a9efdb4159c"  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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''&#916;yrbC722::kan''
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PMID:16738554
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[[cgscmutation:106044|CGSC:106044]]
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''mlaC(del)''
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Growth Phenotype
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Increase outer membrane permeability.
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PMID:19383799
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Parental Strain: JCM158, a Derivative from the Keo Collection.
Experimental Strain: JCM528
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Figure 1 and 3. 
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''&#916;yrbC722::kan''
''mlaC(del)'' ''pldA''
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Growth Phenotype
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Increase outer membrane permeability. Increase was more than single gene mutations.
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PMID:16738554
PMID:19383799
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[[cgscmutation:106044|CGSC:106044]]
Parental Strain: JCM158, a deriv in the Keo collection.
 
Experimental Strain: JCM736
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Figure 1 and 3.  


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****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="Y4e04bf53524a0"  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="Y4e04bf53524a0"  class=" tableEdit Genetic_interaction_table dataTable"   
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|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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Primer 2:CCTTTTTTCTCTTCCAGAGTGAT  
Primer 2:CCTTTTTTCTCTTCCAGAGTGAT  
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[[:Category:Kohara_Phage:14F11|14F11]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=521 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:7E3|7E3]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=522 Genobase]
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PMID:3038334
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****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="J46a9efdc9b36e"  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="J46a9efdc9b36e"  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]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7659 EcoCyc:G7659]
[http://chase.ou.edu/macro/searchlink.php?bnum=b3192 EcoliGenExpDB:b3192]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2650 EchoBASE:EB2650]
[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
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[http://chase.ou.edu/macro/searchlink.php?bnum=b3192 EcoliGenExpDB:b3192]
[http://BioCyc.org/ECOO157/new-image?object=YRBC ECOO157CYC:YRBC]
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[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
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[http://BioCyc.org/ECOL199310/new-image?object=C3952 ECOL199310CYC:C3952]
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[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12798 EcoGene:EG12798]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7659 ECOCYC:G7659]
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Escherichia coli str. K-12 substr. 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=YRBC ECOO157CYC:YRBC]
[http://www.ncbi.nlm.nih.gov/gene?term=947710 GeneID:947710]
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Escherichia coli str. K-12 substr. MG1655
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[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[RegulonDB]]
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[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0010489&formSubmitReturn=1 ASAP:ABE-0010489]
RegulonDB:
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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Latest revision as of 20:46, 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

mlaC

Mnemonic
Synonyms

ECK3181, b3192, JW3159, yrbC[1], JW3159, yrbC

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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

71.89 minutes 

MG1655: 3335913..3335278
<gbrowseImage> name=NC_000913:3335278..3335913 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 3273126..3272491
<gbrowseImage> name=NC_012967:3272491..3273126 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3222426..3223061
<gbrowseImage> name=NC_012759:3222426..3223061 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3337746..3337111
<gbrowseImage> name=NC_007779:3337111..3337746 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3433658..3433023
<gbrowseImage> name=NC_010473:3433023..3433658 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

ΔyrbC722::kan

PMID:16738554[2]

CGSC:106044

mlaC(del)

Growth Phenotype

Increase outer membrane permeability.

PMID:19383799[3]

Parental Strain: JCM158, a Derivative from the Keo Collection.

Experimental Strain: JCM528

Figure 1 and 3.

ΔyrbC (Keio:JW3159)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC10397[4]

mlaC(del) pldA

Growth Phenotype

Increase outer membrane permeability. Increase was more than single gene mutations.

PMID:19383799[3]

Parental Strain: JCM158, a deriv in the Keo collection.

Experimental Strain: JCM736

Figure 1 and 3.

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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

JW3159

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTTAAACGTTTAATGATGGT

Primer 2:CCTTTTTTCTCTTCCAGAGTGAT

14F11

Kohara Phage

Genobase

PMID:3038334[6]

7E3

Kohara Phage

Genobase

PMID:3038334[6]

sfsB203::Tn10

Linked marker

CAG12072 = CGSC7440[4]

est. P1 cotransduction: 88% [7]
Synonyms:zgj-203::Tn10, zha-203::Tn10

zhc-6::Tn10

Linked marker

CAG12153 = CGSC7442[4]

est. P1 cotransduction: 33% [7]
Synonyms:zha-6::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

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3192

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3952

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YRBC

EcoCyc (EcoliWiki Page)

ECOCYC:G7659

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947710

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

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 Malinverni, JC & Silhavy, TJ (2009) An ABC transport system that maintains lipid asymmetry in the gram-negative outer membrane. Proc. Natl. Acad. Sci. U.S.A. 106 8009-14 PubMed
  4. ↑ 4.0 4.1 4.2 CGSC: The Coli Genetics Stock Center
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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