ompG:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older edit
Adding section & Genetic interactions table to Gene pages.
touch
 
(10 intermediate revisions by 2 users not shown)
Line 46: Line 46:
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1315, b1319, JW1312''<ref name='LIB:Riley_2006'/>
''ECK1315, b1319, JW1312''<ref name='LIB:Riley_2006'/>, JW1312''


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 67: Line 67:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="G46a9c493ad624"  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="G46a9c493ad624"  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
Line 78: Line 78:
MG1655: 1379971..1380876<br /><gbrowseImage>
MG1655: 1379971..1380876<br /><gbrowseImage>
name=NC_000913:1379971..1380876
name=NC_000913:1379971..1380876
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
Line 84: Line 84:
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6657 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6657 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|1378971|1381876|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|1378971|1381876|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|1379971|1380876|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|1379971|1380876|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6657 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6657 EcoCyc Sequence Dump]  
|-  
|-  
Line 118: Line 118:


|
|
{{GBrowseLink|BW2952|012759|1270820|NC_1271725|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|1270820|1271725|GBrowse (BW2952)}}
|
|
{{GBrowseFastaLink|BW2952|012759|1270820|NC_1271725|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|1270820|1271725|FASTA Dump}}  
|-  
|-  
|
|
Line 128: Line 128:
|
|
W3110: 1383661..1384566<br /><gbrowseImage>
W3110: 1383661..1384566<br /><gbrowseImage>
name=AC_000091:1383661..1384566
name=NC_007779:1383661..1384566
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1382661|1385566|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|1382661|1385566|GBrowse(W3110)}}  
|
|
{{GBrowseFastaLink|ecoli_W3110|AC_000091|1383661|1384566|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|1383661|1384566|FASTA Dump}}  
|-  
|-  
|
|
Line 145: Line 145:
DH10B: 1469367..1470272<br /><gbrowseImage>
DH10B: 1469367..1470272<br /><gbrowseImage>
name=NC_010473:1469367..1470272
name=NC_010473:1469367..1470272
source=ecoli_DH10B
source=DH10B
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


|
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1467557|1472082|GBrowse(DH10B)}}
{{GBrowseLink|DH10B|NC_010473|1467557|1472082|GBrowse(DH10B)}}
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1467557|1472082|FASTA Dump}}  
{{GBrowseFastaLink|DH10B|NC_010473|1467557|1472082|FASTA Dump}}  


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 172: Line 172:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="H46a9c4945b153"  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="H46a9c4945b153"  class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
Line 207: Line 207:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="P46a9c4949cf8f"  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="P46a9c4949cf8f"  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
Line 247: Line 247:
*  
*  
****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="S4e04c07e96a07"  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="S4e04c07e96a07"  class=" tableEdit Genetic_interaction_table dataTable"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
Line 268: Line 268:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="B46a9c4954ab53"  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="B46a9c4954ab53"  class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
Line 286: Line 286:


Primer 2:CCGAACGAGTAATTTACGCCGAC  
Primer 2:CCGAACGAGTAATTTACGCCGAC  
|-
|
[[:Category:Kohara_Phage:2D3|2D3]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=258 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:3H8|3H8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=259 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6B4|6B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=260 Genobase]
|
PMID:3038334
|-  
|-  
|
|
Line 325: Line 352:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="V46a9c495d7c4f"  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="V46a9c495d7c4f"  class=" tableEdit Gene_accessions_table"   
|- {{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=G6657 EcoCyc:G6657]
EcoCyc:G6657
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3202 EchoBASE:EB3202]
EcoGene:EG13428
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1319 EcoliGenExpDB:b1319]
RegulonDB:ECK120003252
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1791 ECOL199310CYC:C1791]
[http://www.ncbi.nlm.nih.gov/gene?term=945889 GeneID:945889]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13428 EcoGene:EG13428]
EchoBASE:EB3202
|
|
''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=OMPG ECOO157CYC:OMPG]
ASAP:ABE-0004425
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]  
|-  
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0004425&formSubmitReturn=1 ASAP:ABE-0004425]
|


|- class="tableEdit_footer"  
|- class="tableEdit_footer"  
Line 396: Line 416:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|   id="M46a6e20fde77b"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a6e20fde77b"  class=" tableEdit Links_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:29, 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

[back to top]


See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

ompG

Mnemonic

Outer membrane protein

Synonyms

ECK1315, b1319, JW1312[1], JW1312

edit table


Notes

Location(s) and DNA Sequence

[back to top]


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

29.74 minutes 

MG1655: 1379971..1380876
<gbrowseImage> name=NC_000913:1379971..1380876 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1380316..1381221
<gbrowseImage> name=NC_012967:1380316..1381221 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1270820..1271725
<gbrowseImage> name=NC_012759:1270820..1271725 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1383661..1384566
<gbrowseImage> name=NC_007779:1383661..1384566 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1469367..1470272
<gbrowseImage> name=NC_010473:1469367..1470272 source=DH10B preset=GeneLocation </gbrowseImage>

edit table


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

1380034

Edman degradation

PMID:9721282[2]


edit table


Notes

Alleles and Phenotypes

[back to top]


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

ΔompG (Keio:JW1312)

deletion

deletion

PMID:16738554[3]

Shigen


edit table


Notes

Genetic Interactions

[back to top]



Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table


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

JW1312

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAAAGTTATTACCCTGTAC

Primer 2:CCGAACGAGTAATTTACGCCGAC

2D3

Kohara Phage

Genobase

PMID:3038334[5]

3H8

Kohara Phage

Genobase

PMID:3038334[5]

6B4

Kohara Phage

Genobase

PMID:3038334[5]

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[6]

est. P1 cotransduction: 68% [7]
Synonyms:zci-233::Tn10

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[6]

est. P1 cotransduction: 30% [7]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

edit table


Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoCyc

EcoCyc:G6657

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG13428

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003252

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945889

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB3202

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004425

Escherichia coli str. K-12 substr. MG1655

edit table


Notes

Links

[back to top]



<protect>

References

[back to top]


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. ↑ Fajardo, DA et al. (1998) Biochemistry and regulation of a novel Escherichia coli K-12 porin protein, OmpG, which produces unusually large channels. J. Bacteriol. 180 4452-9 PubMed
  3. ↑ 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. ↑ 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
  5. ↑ 5.0 5.1 5.2 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
  6. ↑ 6.0 6.1 CGSC: The Coli Genetics Stock Center
  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

Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=ompG:Gene&oldid=1476366"