yaeF: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="K46a9aa8a2bf48" class=" tableEdit Gene_nomenclature_table"


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


|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left |Synonyms
||
||
''ECK0193, b0193, JW5016, yaeK''<ref name='LIB:Riley_2006'/>
''ECK0193, b0193, JW5016, yaeK''<ref name='LIB:Riley_2006'/>


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48&page=10963&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table] ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48&page=10963&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.K46a9aa8a2bf48-->
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="T46a9aa8aa46f0" 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|216179|217003|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|216179|217003|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12138 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12138 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 219021..219845<br />{{GBrowseFigureByCoord|219021|219845|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|219021|219845|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|219021|219845|FASTA Dump}}
|-  
|-  
|
|
Line 104: Line 115:
|
|
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|188635|192755|FASTA Dump}}  
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|188635|192755|FASTA Dump}}  
|-
|
[[REL606]]
|
|
NC_012967: 219021..219845<br />{{GBrowseFigureByCoord|219021|219845|REL606|NC_012967}}
|
{{GBrowseLink|REL606|NC_012967|219021|219845|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|219021|219845|FASTA Dump}}


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.T46a9aa8aa46f0&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table] || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.T46a9aa8aa46f0&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_location_table edit table]</span> || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.T46a9aa8aa46f0-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.T46a9aa8aa46f0-->
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="I46a9aa8b4da4c" 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=421aa90e079fa326b6494f812ad13e79.10963.I46a9aa8b4da4c&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.I46a9aa8b4da4c&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_sequence_features_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.I46a9aa8b4da4c-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.I46a9aa8b4da4c-->
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="V46a9aa8b8e7c5" 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 245: Line 245:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.V46a9aa8b8e7c5&page=10963&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table] || || || || || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.V46a9aa8b8e7c5&page=10963&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.V46a9aa8b8e7c5-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.V46a9aa8b8e7c5-->
Line 263: Line 263:
*  
*  
****************************************************************************************** -->{{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="X46a9aa8c37204" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
|-
!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
|-  
|-  
Line 301: Line 301:
Synonyms:zae-502::Tn10  
Synonyms:zae-502::Tn10  


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.X46a9aa8c37204&page=10963&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table] || || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.X46a9aa8c37204&page=10963&pagename={{FULLPAGENAMEE}}&type=&template=Gene_resource_table edit table]</span> || || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.X46a9aa8c37204-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.X46a9aa8c37204-->
Line 319: Line 319:
*  
*  
****************************************************************************************** -->{{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="W46a9aa8cc0c63" class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|-
!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
Line 372: Line 372:
   
   


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.W46a9aa8cc0c63&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.W46a9aa8cc0c63&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Gene_accessions_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.W46a9aa8cc0c63-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.W46a9aa8cc0c63-->
Line 390: Line 390:
*  
*  
****************************************************************************************** -->
****************************************************************************************** -->
{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{|   id="K46a677c496282" class=" tableEdit Links_table"   
|- {{table_heading_style}}
|-
!|Name!!URL!!Comments
!|Name!!URL!!Comments


|-class='sortbottom'
|- class="tableEdit_footer"
|[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a677c496282&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table] || ||
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.10963.K46a677c496282&page=10963&pagename={{FULLPAGENAMEE}}&type=0&template=Links_table edit table]</span> || ||
|}
|}
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.K46a677c496282-->
<!--box uid=421aa90e079fa326b6494f812ad13e79.10963.K46a677c496282-->

Revision as of 01:16, 10 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

yaeF

Mnemonic
Synonyms

ECK0193, b0193, JW5016, yaeK[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

4.66 minutes 

MG1655: 217003..216179
gbrowse_img.php?coord=216179..217003&genome=ecoli&name=MG1655&trackset=0&width=300&.png

REL606

NC_012967: 219021..219845
gbrowse_img.php?coord=219021..219845&genome=REL606&name=NC_012967&trackset=0&width=300&.png

W3110

 

W3110: 217003..216179
gbrowse_img.php?coord=216179..217003&genome=ecoli_W3110&name=W3110&trackset=0&width=300&.png

DH10B

DH10B: 191107..190283
gbrowse_img.php?coord=190283..191107&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

ΔyaeF (Keio:JW5016)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11130[3]

yaeF::Tn5KAN

PMID:12519969[4]

ASAP

At position 155 in Minus orientation, contains plasmid pKD46.
ASAP strain name: FB20035

yaeF-1::FLKP2(lacZ,kan,Plac)

PMID:12142427[5]

CGSC:87198

ΔyaeF-2

PMID:12142427[5]

CGSC:87200

ΔyaeF-790::kan

PMID:16738554[2]

CGSC:103480


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

JW5016

Plasmid clone

Shigen

PMID:16769691[6]

Status:Clone OK

Primer 1:GCCGATAAACCAAAGGCGTACTG

Primer 2:CCaCGGGTCAAACCAACAAAGCG

zad-220::Tn10

Linked marker

CAG12025 = CGSC7326[3]

est. P1 cotransduction: 2% [7]

yafC502::Tn10

Linked marker

CAG18436 = CGSC7328[3]

est. P1 cotransduction: 57% [7]
Synonyms:zae-502::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:EG12138

EchoBASE (EcoliWiki Page)

EchoBASE:EB2059

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0193

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0234

EcoGene (EcoliWiki Page)

EcoGene:EG12138

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YAEF

ASAP (EcoliWikiPage)

ASAP:ABE-0000655


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. ↑ Glasner, JD et al. (2003) ASAP, a systematic annotation package for community analysis of genomes. Nucleic Acids Res. 31 147-51 PubMed
  5. ↑ 5.0 5.1 Merlin, C et al. (2002) Tools for characterization of Escherichia coli genes of unknown function. J. Bacteriol. 184 4573-81 PubMed
  6. ↑ 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
  7. ↑ 7.0 7.1 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=yaeF:Gene&oldid=1018548"