nikR:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Data loaded by TableEdit_Loader.
Automated update of mnemonics from EcoGene.
Line 34: Line 34:


|-
|-
!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''nikR''  
''nikR''
|-
|-
!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
Nickel
|-
|-
!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>
''ECK3465, b3481, JW3446, yhhG''<ref name='LIB:Riley_2006'/>
Line 66: Line 66:
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|  id="C46a9f6fe5753b"  class=" tableEdit Gene_location_table"   
{|  id="C46a9f6fe5753b"  class=" tableEdit Gene_location_table"   
|-
|- {{table_heading_style}}
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
|-  
|-  
Line 135: Line 135:
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|  id="I46a9f6ff18fab"  class=" tableEdit Gene_sequence_features_table"   
{|  id="I46a9f6ff18fab"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


Line 213: Line 213:
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|  id="O46a9f70023df1"  class=" tableEdit Gene_resource_table"   
{|  id="O46a9f70023df1"  class=" tableEdit Gene_resource_table"   
|-
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 269: Line 269:
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|  id="E46a9f700c1aa7"  class=" tableEdit Gene_accessions_table"   
{|  id="E46a9f700c1aa7"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 340: Line 340:
****************************************************************************************** -->
****************************************************************************************** -->
{|  id="T46a711d1c57e2"  class=" tableEdit Links_table"   
{|  id="T46a711d1c57e2"  class=" tableEdit Links_table"   
|-
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 21:30, 25 February 2010

{{#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 Alleles and Phenotypes 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

nikR

Mnemonic

Nickel

Synonyms

ECK3465, b3481, JW3446, yhhG[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

77.95 minutes 

MG1655: 3616611..3617012
gbrowse_img.php?coord=3616611..3617012&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3549276..3549677
gbrowse_img.php?coord=3549276..3549677&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4021827..4021426
gbrowse_img.php?coord=4021426..4021827&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3714356..3714757
gbrowse_img.php?coord=3714356..3714757&genome=ecoli_DH10B&name=DH10B&trackset=0&width=300&.png

edit table


Notes

Sequence Features

[back to top]


See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature type Location Description
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

ΔnikR (Keio:JW3446)

deletion

deletion

PMID:16738554[2]

Shigen

nikRR3A

R3A

Loss of DNA-binding

seeded from UniProt:P0A6Z6

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

JW3446

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCCAACGAGTCACCATCACGCT

Primer 2:CCATCTTCCTTCGGCAAGCACTG

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 38% [5]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[4]

est. P1 cotransduction: % [5]

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:EG11519

EchoBASE (EcoliWiki Page)

EchoBASE:EB1481

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3481

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4274

EcoGene (EcoliWiki Page)

EcoGene:EG11519

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YHHG

ASAP (EcoliWikiPage)

ASAP:ABE-0011366


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. ↑ 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
  3. ↑ 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
  4. ↑ 4.0 4.1 CGSC: The Coli Genetics Stock Center
  5. ↑ 5.0 5.1 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=nikR:Gene&oldid=1056580"