ompL:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ompL}}{{Tab On|Gene|ompL}}{{Tab|Gene Product(s)|ompL}}{{Tab|Expression|ompL}}{{Tab|Evolution|ompL}}{{Tab|On One Page|ompL}}{{TabsBottom}}
{{Tab|Quickview|ompL}}{{Tab On|Gene|ompL}}{{Tab|Gene Product(s)|ompL}}{{Tab|Expression|ompL}}{{Tab|Evolution|ompL}}{{Tab|On One Page|ompL}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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{|   id="T46aa012956ee4"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''ompL''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''ompL''
Outer membrane protein
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3868, b3875, JW3846, yshA''<ref name='LIB:Riley_2006'/>, yshA''


|-
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!{{table_heading_style}} |Synonyms
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''ECK3868, b3875, JW3846, yshA''<ref name='LIB:Riley_2006'/>
|-
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<!--Nomenclature_notes--></protect>
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===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<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="L46aa0129d9573"  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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|
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MG1655
MG1655
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87.54 minutes&nbsp;
87.54 minutes&nbsp;
|
|
MG1655: 4062318..4061626<br />{{GBrowseFigureByCoord|4060626|4063318|ecoli|MG1655}}
MG1655: 4062318..4061626<br /><gbrowseImage>
name=NC_000913:4061626..4062318
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7814 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7814 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:4060626..4063318 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|4060626|4063318|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:4061626..4062318&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|4061626|4062318|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7814 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7814 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 4041861..4042553<br /><gbrowseImage>
name=NC_012967:4041861..4042553
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|4041861|4042553|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4041861|4042553|FASTA Dump}}
|-
|
[[BW2952]]
|
 
|
NC_012759: 3951295..3951987<br /><gbrowseImage>
name=NC_012759:3951295..3951987
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|3951295|3951987|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|3951295|3951987|FASTA Dump}}
|-  
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 3572386..3573078<br />{{GBrowseFigureByCoord|3571386|3574078|ecoli_W3110|W3110}}  
W3110: 3572386..3573078<br /><gbrowseImage>
name=NC_007779:3572386..3573078
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|3571386|3574078|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|3572386|3573078|FASTA Dump}}  
|-
|
[[DH10B]]
|
 
|
DH10B: 4161238..4160546<br /><gbrowseImage>
name=NC_010473:4160546..4161238
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:3571386..3574078 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|4159162|4162622|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:3572386..3573078&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|4159162|4162622|FASTA Dump}}
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46aa012a9e795"  class=" tableEdit Gene_sequence_features_table" 
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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Coding Start (SO:0000323)
|
[[MG1655]]
|
4061629
|
Edman degradation
|
PMID:11080145<br />
|
 
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46aa012ae8d0e"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
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&Delta;ompL (Keio:JW3846)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109060 CGSC10779]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;ompL737::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102180|CGSC:102180]]
|
 
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="N4e04c07fb0023"  class=" tableEdit Genetic_interaction_table dataTable" 
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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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JW3846
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCAAAAAGATTAATGCAATAAT
 
Primer 2:CCGAAGAAATACTTCGTCCCGAT
|-
|
[[:Category:Kohara_Phage:9H1|9H1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=545 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:10F1|10F1]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=546 Genobase]
|
PMID:3038334
|-
|
[[fadA:Gene|fad-751::Tn10]]
|
Linked marker
|
CAG18496 = [http://cgsc2.biology.yale.edu/Strain.php?ID=40344 CGSC7465]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:fadAB101::Tn10
|-
|
[[yihO:Gene|zih-35::Tn10]]
|
Linked marker
|
CAG18495 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37140 CGSC7467]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 91% <ref name='LIB:Nichols_linked_Tn'/>
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
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|-
|
[[EcoCyc]]
|
EcoCyc:G7814
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7814 EcoCyc:G7814] 
EcoGene:EG13374
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3156 EchoBASE:EB3156] 
RegulonDB:ECK120004316
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b3875 EcoliGenExpDB:b3875]
[http://www.ncbi.nlm.nih.gov/gene?term=948366 GeneID:948366]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13374 EcoGene:EG13374] 
EchoBASE:EB3156
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YSHA ECOO157CYC:YSHA] 
ASAP:ABE-0012659
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
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==References==
==References==
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{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:50, 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

ompL

Mnemonic

Outer membrane protein

Synonyms

ECK3868, b3875, JW3846, yshA[1], yshA

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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

87.54 minutes 

MG1655: 4062318..4061626
<gbrowseImage> name=NC_000913:4061626..4062318 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 4041861..4042553
<gbrowseImage> name=NC_012967:4041861..4042553 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 3951295..3951987
<gbrowseImage> name=NC_012759:3951295..3951987 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3572386..3573078
<gbrowseImage> name=NC_007779:3572386..3573078 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 4161238..4160546
<gbrowseImage> name=NC_010473:4160546..4161238 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

4061629

Edman degradation

PMID:11080145[2]


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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

ΔompL (Keio:JW3846)

deletion

deletion

PMID:16738554[3]

Shigen
CGSC10779[4]

ΔompL737::kan

PMID:16738554[3]

CGSC:102180


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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

JW3846

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAAAAGATTAATGCAATAAT

Primer 2:CCGAAGAAATACTTCGTCCCGAT

9H1

Kohara Phage

Genobase

PMID:3038334[6]

10F1

Kohara Phage

Genobase

PMID:3038334[6]

fad-751::Tn10

Linked marker

CAG18496 = CGSC7465[4]

est. P1 cotransduction: 25% [7]
Synonyms:fadAB101::Tn10

zih-35::Tn10

Linked marker

CAG18495 = CGSC7467[4]

est. P1 cotransduction: 91% [7]

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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:G7814

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13374

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004316

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:948366

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3156

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0012659

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. ↑ Dartigalongue, C et al. (2000) Protein folding in the periplasm in the absence of primary oxidant DsbA: modulation of redox potential in periplasmic space via OmpL porin. EMBO J. 19 5980-8 PubMed
  3. ↑ 3.0 3.1 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
  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).

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