lexA:Gene: Difference between revisions

From EcoliWiki
Jump to navigation Jump to search
← Older editNewer edit →
Data loaded by TableEdit_Loader.
Update TableEdit tables.
Line 31: Line 31:
*  
*  
****************************************************************************************** -->{{Gene_nomenclature_help}}
****************************************************************************************** -->{{Gene_nomenclature_help}}
{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{| id="F46aa058a7e25a" class=" tableEdit Gene_nomenclature_table"


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


|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
||
||
''ECK4035, b4043, JW4003, exrA, tsl, umuA''<ref name='LIB:Riley_2006'/>
''ECK4035, b4043, JW4003, exrA, tsl, umuA''<ref name='LIB:Riley_2006'/>


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.F46aa058a7e25a&page=18645&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.F46aa058a7e25a&page=18645&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.F46aa058a7e25a-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.F46aa058a7e25a-->
Line 65: Line 65:
*  
*  
****************************************************************************************** -->{{Gene_location_help}}
****************************************************************************************** -->{{Gene_location_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="Q46aa058b0e011" 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 82: Line 82:
{{GBrowseFastaLink|ecoli|NC_000913|4255138|4255746|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|4255138|4255746|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG10533 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG10533 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 4236047..4236655<br />{{GBrowseFigureByCoord|4236047|4236655|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|4236047|4236655|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4236047|4236655|FASTA Dump}}
|-  
|-  
|
|
Line 104: Line 115:
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4353618|4356658|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|4353618|4356658|FASTA Dump}}  
|-
|
[[REL606]]
|
|
NC_012967: 4236047..4236655<br />{{GBrowseFigureByCoord|4236047|4236655|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|4236047|4236655|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|4236047|4236655|FASTA Dump}}


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.Q46aa058b0e011&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.Q46aa058b0e011&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.Q46aa058b0e011-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.Q46aa058b0e011-->
Line 134: Line 134:
*  
*  
****************************************************************************************** -->{{Gene_sequence_features_help}}
****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="L46aa058bc99aa" class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|-
!|Feature type!!Location!!Description
!|Feature type!!Location!!Description


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.L46aa058bc99aa&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.L46aa058bc99aa&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.L46aa058bc99aa-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.L46aa058bc99aa-->
Line 156: Line 156:
*  
*  
****************************************************************************************** -->{{Gene_alleles_help}}
****************************************************************************************** -->{{Gene_alleles_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{|   id="D46aa058c206f8" 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 416: Line 416:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.D46aa058c206f8&page=18645&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.D46aa058c206f8&page=18645&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.D46aa058c206f8-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.D46aa058c206f8-->
Line 434: Line 434:
*  
*  
****************************************************************************************** -->{{Gene_resources_help}}
****************************************************************************************** -->{{Gene_resources_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="K46aa058cdba1d" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|-
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 471: Line 471:
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 9% <ref name='LIB:Nichols_linked_Tn'/>  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.K46aa058cdba1d&page=18645&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.K46aa058cdba1d&page=18645&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.K46aa058cdba1d-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.K46aa058cdba1d-->
Line 489: Line 489:
*  
*  
****************************************************************************************** -->{{Gene_accessions_help}}
****************************************************************************************** -->{{Gene_accessions_help}}
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="A46aa058d892be" class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|-
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 549: Line 549:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.A46aa058d892be&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.A46aa058d892be&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.A46aa058d892be-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.A46aa058d892be-->
Line 567: Line 567:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="D46a71ecf03b0b" class=" tableEdit Links_table"   
|- {{table_heading_style}}
|-
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.D46a71ecf03b0b&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.18645.D46a71ecf03b0b&page=18645&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.D46a71ecf03b0b-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.18645.D46a71ecf03b0b-->

Revision as of 01:56, 9 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

lexA

Mnemonic
Synonyms

ECK4035, b4043, JW4003, exrA, tsl, umuA[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

91.71 minutes 

MG1655: 4255138..4255746
gbrowse_img.php?coord=4255138..4255746&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 4236047..4236655
gbrowse_img.php?coord=4236047..4236655&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 4260705..4261313
gbrowse_img.php?coord=4260705..4261313&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 4354834..4355442
gbrowse_img.php?coord=4354834..4355442&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

spr

PMID:2834329[2] PMID:7038393[3]

uninducible, not cleaved during SOS response

lexA107

CGSC:6267

lexA1(Ind-)

non-inducible SOS response

CGSC:9237

lexA41(ts)

temperature sensitive

CGSC:9601

lexA3(Ind-)

non-inducible SOS response

CGSC:9602

lexA51

CGSC:10280

lexA101

CGSC:11964

lexA102

CGSC:11979

lexA109

CGSC:11985

lexA103

CGSC:14425

lexA104

CGSC:14427

lexA105

CGSC:14429

lexA106

CGSC:14431

lexA108

CGSC:14439

lexA71::Tn5

CGSC:30813


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

JW4003

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCAAAGCGTTAACGGCCAGGCA

Primer 2:CCaAGCCAGTCGCCGTTGCGAAT

malF3089::Tn10

Linked marker

CAG12164 = CGSC7476[5]

est. P1 cotransduction: 60% [6]

zje-2241::Tn10

Linked marker

CAG18427 = CGSC7481[5]

est. P1 cotransduction: 9% [6]

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:EG10533

EchoBASE (EcoliWiki Page)

EchoBASE:EB0528

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b4043

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C5014

EcoGene (EcoliWiki Page)

EcoGene:EG10533

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:LEXA

CGSC (EcoliWiki Page)

CGSC:558

ASAP (EcoliWikiPage)

ASAP:ABE-0013241


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. ↑ Lin, LL & Little, JW (1988) Isolation and characterization of noncleavable (Ind-) mutants of the LexA repressor of Escherichia coli K-12. J. Bacteriol. 170 2163-73 PubMed
  3. ↑ Froehlich, B (1981) Weigle reactivation of the single-stranded DNA phage f1. Mol. Gen. Genet. 184 416-20 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 CGSC: The Coli Genetics Stock Center
  6. ↑ 6.0 6.1 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=lexA:Gene&oldid=981366"