asd: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
||
||
''asd''  
''asd''  
|-
|-
!align=left |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||


|-
|-
!align=left |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK3419, b3433, JW3396, dap, hom, dap+hom''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
''ECK3419, b3433, JW3396, dap, hom, dap+hom''<ref name='LIB:Riley_2006'/><ref name='LIB:EcoCyc10.6'/>
Line 66: Line 66:
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|  id="G46a9f5ce36321"  class=" tableEdit Gene_location_table"   
{|  id="G46a9f5ce36321"  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 88: Line 88:


|
|
NC_012967: 3505229..3506332<br />{{GBrowseFigureByCoord|3505229|3506332|REL606|NC_012967}}
NC_012967: 3506332..3505229<br />{{GBrowseFigureByCoord|3505229|3506332|REL606|NC_012967}}
|
|
{{GBrowseLink|REL606|NC_012967|3505229|3506332|GBrowse (REL606)}}
{{GBrowseLink|REL606|NC_012967|3505229|3506332|GBrowse (REL606)}}
Line 135: Line 135:
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|  id="R46a9f5ceeba57"  class=" tableEdit Gene_sequence_features_table"   
{|  id="R46a9f5ceeba57"  class=" tableEdit Gene_sequence_features_table"   
|-
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|   id="Q46a9f5cf4079a"  class=" tableEdit Gene_allele_table"   
{| {{Prettytable}}  id="Q46a9f5cf4079a"  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 196: Line 196:
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|  id="P46a9f5d002791"  class=" tableEdit Gene_resource_table"   
{|  id="P46a9f5d002791"  class=" tableEdit Gene_resource_table"   
|-
|- {{table_heading_style}}
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 253: Line 253:
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|  id="D46a9f5d09fa7e"  class=" tableEdit Gene_accessions_table"   
{|  id="D46a9f5d09fa7e"  class=" tableEdit Gene_accessions_table"   
|-
|- {{table_heading_style}}
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 331: Line 331:
****************************************************************************************** -->
****************************************************************************************** -->
{|  id="S46a710be9393e"  class=" tableEdit Links_table"   
{|  id="S46a710be9393e"  class=" tableEdit Links_table"   
|-
|- {{table_heading_style}}
!|Name!!URL!!Comments
!|Name!!URL!!Comments


Revision as of 20:10, 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

asd

Mnemonic
Synonyms

ECK3419, b3433, JW3396, dap, hom, dap+hom[1][2]

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

76.98 minutes 

MG1655: 3572901..3571798
gbrowse_img.php?coord=3571798..3572901&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 3506332..3505229
gbrowse_img.php?coord=3505229..3506332&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4065537..4066640
gbrowse_img.php?coord=4065537..4066640&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 3670646..3669543
gbrowse_img.php?coord=3669543..3670646&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

asd-1

CGSC:5115


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

JW3396

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCAAAAATGTTGGTTTTATCGG

Primer 2:CCgGCCAGTTGACGAAGCATCCG

glgP721::Tn10

Linked marker

CAG18638 = CGSC7451[4]

est. P1 cotransduction: 75% [5]
Synonyms:zhg-3086::Tn10, zhh-21::Tn10

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[4]

est. P1 cotransduction: 50% [5]
Synonyms:zhf-50::Tn10, zhf-5::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:EG10088

EchoBASE (EcoliWiki Page)

EchoBASE:EB0086

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b3433

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C4220

EcoGene (EcoliWiki Page)

EcoGene:EG10088

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:ASD

CGSC (EcoliWiki Page)

CGSC:996

ASAP (EcoliWikiPage)

ASAP:ABE-0011211


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. ↑ EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  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=asd:Gene&oldid=1026913"