stfR:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Update TableEdit tables.
Fixing REL gene coord display.
Line 34: Line 34:


|-
|-
!align=left |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''stfR''  
''stfR''  
|-
|-
!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||


|-
|-
!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1367, b1372, JW1366, ynaB''<ref name='LIB:Riley_2006'/>
''ECK1367, b1372, JW1366, ynaB''<ref name='LIB:Riley_2006'/>
Line 66: Line 66:
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|  id="S46a9c5a9acca0"  class=" tableEdit Gene_location_table"   
{|  id="S46a9c5a9acca0"  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 124: Line 124:
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|  id="C46a9c5aa5b4c2"  class=" tableEdit Gene_sequence_features_table"   
{|  id="C46a9c5aa5b4c2"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


Line 145: Line 145:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|   id="L46a9c5aa9d5a3"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="L46a9c5aa9d5a3"  class=" tableEdit Gene_allele_table"   
|-
|- {{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 202: Line 202:
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|  id="V46a9c5ab4bbc6"  class=" tableEdit Gene_resource_table"   
{|  id="V46a9c5ab4bbc6"  class=" tableEdit Gene_resource_table"   
|-
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 258: Line 258:
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|  id="D46a9c5abd8f7c"  class=" tableEdit Gene_accessions_table"   
{|  id="D46a9c5abd8f7c"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 329: Line 329:
****************************************************************************************** -->
****************************************************************************************** -->
{|  id="Z46a6e323113c9"  class=" tableEdit Links_table"   
{|  id="Z46a6e323113c9"  class=" tableEdit Links_table"   
|-
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:51, 21 January 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

stfR

Mnemonic
Synonyms

ECK1367, b1372, JW1366, ynaB[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

30.76 minutes 

MG1655: 1427073..1430435
gbrowse_img.php?coord=1427073..1430435&genome=ecoli&name=MG1655&trackset=0&width=300&.png

W3110

 

W3110: 1430763..1434125
gbrowse_img.php?coord=1430763..1434125&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 1516469..1519831
gbrowse_img.php?coord=1516469..1519831&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

ΔstfR (Keio:JW1366)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9210[3]

ΔstfR735::kan

PMID:16738554[2]

CGSC:103044


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

JW1366

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCGCAGTAAAGATTTCAGGTGT

Primer 2:CCTGCAAGCCTCACAATATAGTT

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[3]

est. P1 cotransduction: 55% [5]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

zhj-3076::Tn10

Linked marker

CAG18640 = CGSC7453[3]

est. P1 cotransduction: 80% [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:G6695

EchoBASE (EcoliWiki Page)

EchoBASE:EB3152

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1372

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C3150

EcoGene (EcoliWiki Page)

EcoGene:EG13370

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:Z1918

ASAP (EcoliWikiPage)

ASAP:ABE-0004595


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. ↑ 2.0 2.1 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. ↑ 3.0 3.1 3.2 CGSC: The Coli Genetics Stock Center
  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 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=stfR:Gene&oldid=1027844"