ispF:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Convert to gbrowse_img.php extension.
Adding section & Genetic interactions table to Gene pages.
Line 16: Line 16:
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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]]
Line 256: Line 257:
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16057.C4e04be02541a5-->
<!--
******************************************************************************************
*
*  ** PLEASE DON'T EDIT THIS TABLE DIRECTLY.  Use the edit table link under the table. **
*
****************************************************************************************** -->{{Genetic_interaction_help}}
{|  id="C4e04be02541a5"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=bc145ea147f7e36caf09c1bfeed4ee9d.16057.C4e04be02541a5&page=16057&pagename={{FULLPAGENAMEE}}&type=0&template=Genetic_interaction_table edit table]</span> || || || || || ||
|}
<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.16057.C4e04be02541a5--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==

Revision as of 16:40, 24 June 2011

{{#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

ispF

Mnemonic

Isoprenoid

Synonyms

ECK2741, b2746, JW2716, ygbB[1]

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

61.84 minutes 

MG1655: 2869802..2869323
<gbrowseImage> name=NC_000913:2869323..2869802 source=ecoli preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 2766641..2766162
<gbrowseImage> name=NC_012967:2766162..2766641 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 2755135..2755614
<gbrowseImage> name=NC_012759:2755135..2755614 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 2870436..2869957
<gbrowseImage> name=AC_000091:2869957..2870436 source=ecoli_W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2962344..2961865
<gbrowseImage> name=NC_010473:2961865..2962344 source=ecoli_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
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

ispFD8S

D8S

Loss of activity

seeded from UniProt:P62617

ispFH42S

H42S

Loss of activity

seeded from UniProt:P62617

ispFD56S

D56S

35% decrease of activity

seeded from UniProt:P62617

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

JW2716

Plasmid clone

Shigen

PMID:16769691[2]

Status:Clone OK

Primer 1:GCCCGAATTGGACACGGTTTTGA

Primer 2:CCTTTTGTTGCCTTAATGAGTAG

srlD3131::Tn10

Linked marker

CAG18642 = CGSC7423[3]

est. P1 cotransduction: 15% [4]
Synonyms:zfh-3131::Tn10, zfi-3131::Tn10

cysI95::Tn10

Linked marker

CAG12173 = CGSC7425[3]

est. P1 cotransduction: 55% [4]
Synonyms:cysC95::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 (EcoliWiki Page)

EcoCyc:EG11816

EchoBASE (EcoliWiki Page)

EchoBASE:EB1763

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b2746

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3313

EcoGene (EcoliWiki Page)

EcoGene:EG11816

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YGBB

ASAP (EcoliWikiPage)

ASAP:ABE-0009013


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. ↑ 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
  3. ↑ 3.0 3.1 CGSC: The Coli Genetics Stock Center
  4. ↑ 4.0 4.1 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=ispF:Gene&oldid=1249724"