scpC: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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''ygfH, ECK2916, b2920, JW2887''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>
''ygfH, ECK2916, b2920, JW2887''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc11.1'/>, JW2887''


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****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|   id="G46a9e96901e22"  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="G46a9e96901e22"  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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MG1655: 3062824..3064302<br /><gbrowseImage>
MG1655: 3062824..3064302<br /><gbrowseImage>
name=NC_000913:3062824..3064302
name=NC_000913:3062824..3064302
source=ecoli
source=MG1655
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7517 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G7517 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3061824|3065302|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3061824|3065302|GBrowse(MG1655)}}
   
   
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{{GBrowseFastaLink|ecoli|NC_000913|3062824|3064302|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3062824|3064302|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G7517 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G7517 EcoCyc Sequence Dump]  
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{{GBrowseLink|BW2952|012759|2949972|NC_2951450|GBrowse (BW2952)}}
{{GBrowseLink|BW2952|NC_012759|2949972|2951450|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|2949972|NC_2951450|FASTA Dump}}  
{{GBrowseFastaLink|BW2952|NC_012759|2949972|2951450|FASTA Dump}}  
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W3110: 3063458..3064936<br /><gbrowseImage>
W3110: 3063458..3064936<br /><gbrowseImage>
name=AC_000091:3063458..3064936
name=NC_007779:3063458..3064936
source=ecoli_W3110
source=W3110
preset=GeneLocation
preset=GeneLocation
</gbrowseImage>
</gbrowseImage>


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{{GBrowseLink|ecoli_W3110|AC_000091|3062458|3065936|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|3062458|3065936|GBrowse(W3110)}}  
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|3063458|3064936|FASTA Dump}}  
{{GBrowseFastaLink|W3110|NC_007779|3063458|3064936|FASTA Dump}}  


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****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|   id="T46a9e969b2b76"  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="T46a9e969b2b76"  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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****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{| {{Prettytable}} id="T46a9e96a05e2f"  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="T46a9e96a05e2f"  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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****************************************************************************************** -->{{Genetic_interaction_help}}
****************************************************************************************** -->{{Genetic_interaction_help}}
{|   id="Y4e04c395d452c"  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="Y4e04c395d452c"  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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****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|   id="R46a9e96ab6ece"  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="R46a9e96ab6ece"  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:  
Primer 2:  
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[[:Category:Kohara_Phage:1A2|1A2]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=471 Genobase]
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PMID:3038334
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[[:Category:Kohara_Phage:6C5|6C5]]
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Kohara Phage
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[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=472 Genobase]
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PMID:3038334


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****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|   id="H46a9e96b5beab"  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="H46a9e96b5beab"  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]])
[[EcoCyc]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G7517 EcoCyc:G7517]
EcoCyc:G7517
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB2800 EchoBASE:EB2800]
EcoGene:EG12973
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b2920 EcoliGenExpDB:b2920]
RegulonDB:ECK120004079
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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]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
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[http://ecogene.org/geneinfo.php?eg_id=EG12973 EcoGene:EG12973]
[http://www.ncbi.nlm.nih.gov/gene?term=947402 GeneID:947402]
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Escherichia coli str. K-12 substr. MG1655
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
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[http://BioCyc.org/ECOO157/new-image?object=YGFH ECOO157CYC:YGFH]
EchoBASE:EB2800
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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=0009583&formSubmitReturn=1 ASAP:ABE-0009583]
ASAP:ABE-0009583
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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{|   id="O46a705776dee6"  class=" tableEdit Links_table"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="O46a705776dee6"  class=" tableEdit Links_table"   
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!|Name!!URL!!Comments
!|Name!!URL!!Comments

Latest revision as of 20:45, 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

scpC

Mnemonic

SuCcinate to Proprionate conversion

Synonyms

ygfH, ECK2916, b2920, JW2887[1][2], JW2887

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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

66.01 minutes 

MG1655: 3062824..3064302
<gbrowseImage> name=NC_000913:3062824..3064302 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2950553..2952031
<gbrowseImage> name=NC_012967:2950553..2952031 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2949972..2951450
<gbrowseImage> name=NC_012759:2949972..2951450 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 3063458..3064936
<gbrowseImage> name=NC_007779:3063458..3064936 source=W3110 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

ΔscpC771::kan

PMID:16738554[3]

CGSC:106344


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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

Plasmid clone

Shigen

PMID:16769691[4]

Status:

Primer 1:

Primer 2:

1A2

Kohara Phage

Genobase

PMID:3038334[5]

6C5

Kohara Phage

Genobase

PMID:3038334[5]

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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:G7517

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG12973

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120004079

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947402

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB2800

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009583

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. ↑ EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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 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

Categories

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