ompX:Gene: Difference between revisions

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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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{|   id="M46a9b94aa93df" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''ompX''  
''ompX''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Outer membrane protein
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
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''ECK0803, b0814, JW0799, ompP, ybiG, G8003''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK0803, b0814, JW0799, ompP, ybiG, G8003''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>


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*  
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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9b94b2d110"  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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18.31 minutes&nbsp;
18.31 minutes&nbsp;
|
|
MG1655: 849673..850188<br />{{GBrowseFigureByCoord|849673|850188|ecoli|MG1655}}
MG1655: 849673..850188<br /><gbrowseImage>
name=NC_000913:849673..850188
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12117 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12117 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|848673|851188|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|848673|851188|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|849673|850188|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|849673|850188|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12117 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12117 EcoCyc Sequence Dump]  
|-  
|-  
|
|
W3110
[[REL606]]
|
|
&nbsp;
 
|
|
W3110: 850872..851387<br />{{GBrowseFigureByCoord|850872|851387|ecoli_W3110|W3110}}
NC_012967: 843075..843590<br /><gbrowseImage>
name=NC_012967:843075..843590
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|849872|852387|GBrowse(W3110)}}  
{{GBrowseLink|REL606|NC_012967|843075|843590|GBrowse (REL606)}}
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|850872|851387|FASTA Dump}}  
{{GBrowseFastaLink|REL606|NC_012967|843075|843590|FASTA Dump}}  
|-  
|-  
|
|
[[DH10B]]
[[BW2952]]
|
 
|
|
NC_012759: 752641..753156<br /><gbrowseImage>
name=NC_012759:752641..753156
source=BW2952
preset=GeneLocation
</gbrowseImage>


|
|
DH10B: 903601..904116<br />{{GBrowseFigureByCoord|903601|904116|ecoli_DH10B|DH10B}}
{{GBrowseLink|BW2952|NC_012759|752641|753156|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|NC_012759|752641|753156|FASTA Dump}}  
|-
|
W3110
|
&nbsp;
|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|902571|905146|GBrowse(DH10B)}}
W3110: 850872..851387<br /><gbrowseImage>
name=NC_007779:850872..851387
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|902571|905146|FASTA Dump}}  
{{GBrowseLink|W3110|NC_007779|849872|852387|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|850872|851387|FASTA Dump}}  
|-  
|-  
|
|
[[REL606]]
[[DH10B]]
|
|


|
|
NC_012967: 843075..843590<br />{{GBrowseFigureByCoord|843075|843590|REL606|NC_012967}}
DH10B: 903601..904116<br /><gbrowseImage>
name=NC_010473:903601..904116
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|REL606|NC_012967|843075|843590|GBrowse (REL606)}}
{{GBrowseLink|DH10B|NC_010473|902571|905146|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|REL606|NC_012967|843075|843590|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|902571|905146|FASTA Dump}}  


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*  
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****************************************************************************************** -->{{Gene_sequence_features_help}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9b94bca577"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-
|
Coding Start (SO:0000323)
|
[[MG1655]]
|
849742
|
Edman degradation
|
PMID:9629924<br />
|


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*  
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****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="I46a9b94c16689"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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Primer 2:CCGAAGCGGTAACCAACACCGGC  
Primer 2:CCGAAGCGGTAACCAACACCGGC  
|-
|
[[:Category:Kohara_Phage:10A8|10A8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=205 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:4C6|4C6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=206 Genobase]
|
PMID:3038334
|-  
|-  
|
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Synonyms:zbj-1230::Tn10  
Synonyms:zbj-1230::Tn10  


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|- {{table_heading_style}}
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12117 EcoCyc:EG12117]
|
|-
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2056 EchoBASE:EB2056]
EcoCyc:EG12117
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0814 EcoliGenExpDB:b0814]
EcoGene:EG12117
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0900 ECOL199310CYC:C0900]
RegulonDB:ECK120002021
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG12117 EcoGene:EG12117]
[http://www.ncbi.nlm.nih.gov/gene?term=944967 GeneID:944967]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=OMPX ECOO157CYC:OMPX]
EchoBASE:EB2056
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[ASAP]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0002784&formSubmitReturn=1 ASAP:ABE-0002784]
ASAP:ABE-0002784
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:omp genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

ompX

Mnemonic

Outer membrane protein

Synonyms

ECK0803, b0814, JW0799, ompP, ybiG, G8003[1][2]

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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

18.31 minutes 

MG1655: 849673..850188
<gbrowseImage> name=NC_000913:849673..850188 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 843075..843590
<gbrowseImage> name=NC_012967:843075..843590 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 752641..753156
<gbrowseImage> name=NC_012759:752641..753156 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 850872..851387
<gbrowseImage> name=NC_007779:850872..851387 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 903601..904116
<gbrowseImage> name=NC_010473:903601..904116 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

849742

Edman degradation

PMID:9629924[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

ΔompX (Keio:JW0799)

deletion

deletion

PMID:16738554[4]

Shigen


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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

JW0799

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCAAAAAAATTGCATGTCTTTC

Primer 2:CCGAAGCGGTAACCAACACCGGC

10A8

Kohara Phage

Genobase

PMID:3038334[6]

4C6

Kohara Phage

Genobase

PMID:3038334[6]

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[7]

est. P1 cotransduction: 33% [8]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[7]

est. P1 cotransduction: % [8]
Synonyms:zbj-1230::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

EcoCyc

EcoCyc:EG12117

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12117

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002021

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:944967

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2056

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0002784

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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ Molloy, MP et al. (1998) Extraction of membrane proteins by differential solubilization for separation using two-dimensional gel electrophoresis. Electrophoresis 19 837-44 PubMed
  4. ↑ 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. ↑ 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 CGSC: The Coli Genetics Stock Center
  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).

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