fadM:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
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{{Tab|Quickview|ybaW}}{{Tab On|Gene|ybaW}}{{Tab|Gene Product(s)|ybaW}}{{Tab|Expression|ybaW}}{{Tab|Evolution|ybaW}}{{Tab|On One Page|ybaW}}{{TabsBottom}}
{{Tab|Quickview|fadM}}{{Tab On|Gene|fadM}}{{Tab|Gene Product(s)|fadM}}{{Tab|Expression|fadM}}{{Tab|Evolution|fadM}}{{Tab|On One Page|fadM}}{{TabsBottom}}
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|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Alleles and Phenotypes |Alleles and Phenotypes]]
|{{Sub}}[[#Genetic Interactions | Genetic Interactions]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Genetic Resources  |Genetic Resources]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
|{{Sub}}[[#Accessions in Other Databases |Accessions]]
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****************************************************************************************** -->{{Gene_nomenclature_help}}
{|{{Prettytable}}
{|  id="Q46a9b0a076f89"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ybaW''  
''fadM''
|-
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!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
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|-
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!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
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''ECK0437, b0443, JW0433''<ref name='LIB:Riley_2006'/>
''ECK0437, b0443, JW0433'', ybaW, tesC<ref name='LIB:Riley_2006'/>, JW0433, tesC''
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='127552'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="Z46a9b0a12be4c"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
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!Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
!|Strain!!Map location!!Genome coordinates!!Genome browsers!!Sequence links
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MG1655
MG1655
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9.99 minutes&nbsp;
9.99 minutes&nbsp;
|
|
MG1655: 463626..464024<br />{{GBrowseFigureByCoord|462626|465024|ecoli|MG1655}}
MG1655: 463626..464024<br /><gbrowseImage>
name=NC_000913:463626..464024
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6244 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6244 EcoCyc]
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|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:463626..464024&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli|NC_000913|463626|464024|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6244 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6244 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 436469..436867<br /><gbrowseImage>
name=NC_012967:436469..436867
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|436469|436867|GBrowse (REL606)}}
|
{{GBrowseFastaLink|REL606|NC_012967|436469|436867|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 366385..366783<br /><gbrowseImage>
name=NC_012759:366385..366783
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|012759|366385|NC_366783|GBrowse (BW2952)}}
|
{{GBrowseFastaLink|BW2952|012759|366385|NC_366783|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 463626..464024<br />{{GBrowseFigureByCoord|462626|465024|ecoli_W3110|W3110}}  
W3110: 463626..464024<br /><gbrowseImage>
name=NC_007779:463626..464024
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_W3110|NC_007779|462626|465024|GBrowse(W3110)}}
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|463626|464024|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 402957..403355<br /><gbrowseImage>
name=NC_010473:402957..403355
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|462626|465024|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_DH10B|NC_010473|402161|404151|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:463626..464024&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|ecoli_DH10B|NC_010473|402161|404151|FASTA Dump}}
|-class='sortbottom'
 
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===Notes===
===Notes===
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****************************************************************************************** -->{{Gene_sequence_features_help}}
{|class = 'sortable' {{Prettytable}} id='127553'
{|  id="O46a9b0a205432"  class=" tableEdit Gene_sequence_features_table" 
|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
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<protect><!--Sequence_notes--></protect>
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====Notes====
====Notes====
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" {{Prettytable}}
{| {{Prettytable}}  id="S46a9b0a273c80" class=" tableEdit Gene_allele_table dataTable"
|- {{table_heading_style}}
|- {{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
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106877 CGSC8596]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=106877 CGSC8596]<ref name='LIB:cgsc'/>  
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|
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
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[[cgscmutation:103650|CGSC:103650]]
[[cgscmutation:103650|CGSC:103650]]
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|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.11451.S46a9b0a273c80&page=11451&pagename={{FULLPAGENAMEE}}&type=&template=Gene_allele_table edit table]</span> || || || || || || ||
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.11451.B4e04bab752b4e-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="B4e04bab752b4e"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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===Notes===


==Genetic Resources==
==Genetic Resources==
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{|  id="D46a9b0a370070"  class=" tableEdit Gene_resource_table" 
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JW0433
JW0433
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[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
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[[PMID:16769691]]<ref name=PMID:16769691/>
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCCTTAACCATCTGCTCCAGCTT  
Primer 2:CCCTTAACCATCTGCTCCAGCTT  
|-
|-
|
[[:Category:Kohara_Phage:3B6|3B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=148 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:7E2|7E2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=149 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:19B7|19B7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=150 Genobase]
|
PMID:3038334
|-  
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[[ppiD:Gene|zaj-3054::Tn10]]
[[ppiD:Gene|zaj-3054::Tn10]]
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CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
CAG12017 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39373 CGSC7339]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 87% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zba-3054::Tn10  
Synonyms:zba-3054::Tn10  
|-
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[[gsk:Gene|gsk-3055::Tn10]]
[[gsk:Gene|gsk-3055::Tn10]]
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CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
CAG12154 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39379 CGSC7341]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 21% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 21% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10


Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
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===Notes===
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{|class = 'sortable' border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"   
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9b0a459487"  class=" tableEdit Gene_accessions_table"   
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!|Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-  
|-  
|
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])  
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6244 EcoCyc:G6244]
[http://chase.ou.edu/macro/searchlink.php?bnum=b0443 EcoliGenExpDB:b0443]
|
|
   
   
|-  
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])  
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3040 EchoBASE:EB3040]
[http://BioCyc.org/ECOL199310/new-image?object=C0559 ECOL199310CYC:C0559]
|
|
   
   
|-  
|-  
|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
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[http://chase.ou.edu/macro/searchlink.php?bnum=b0443 EcoliGenExpDB:b0443]
[http://BioCyc.org/ECOO157/new-image?object=YBAW ECOO157CYC:YBAW]
|
|
   
   
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0559 ECOL199310CYC:C0559]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6244 ECOCYC:G6244]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13251 EcoGene:EG13251]
[http://www.ncbi.nlm.nih.gov/gene?term=945812 GeneID:945812]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
|
[http://BioCyc.org/ECOO157/new-image?object=YBAW ECOO157CYC:YBAW]
|
|-  
|-  
|
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
[[RegulonDB]]
|
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0001537&formSubmitReturn=1 ASAP:ABE-0001537] 
RegulonDB:
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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===Notes===
===Notes===
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===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yba genes]]
[[Category:yba genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:tes genes]]
[[Category:y genes]]
[[Category:y genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:31, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Alleles and Phenotypes Genetic Interactions Genetic Resources Accessions Links References Suggestions

Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name

fadM

Mnemonic
Synonyms

ECK0437, b0443, JW0433, ybaW, tesC[1], JW0433, tesC

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Notes

Location(s) and DNA Sequence

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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

9.99 minutes 

MG1655: 463626..464024
<gbrowseImage> name=NC_000913:463626..464024 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 436469..436867
<gbrowseImage> name=NC_012967:436469..436867 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 366385..366783
<gbrowseImage> name=NC_012759:366385..366783 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 463626..464024
<gbrowseImage> name=NC_007779:463626..464024 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 402957..403355
<gbrowseImage> name=NC_010473:402957..403355 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

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

Feature Type Strain Genomic Location Evidence Reference Notes
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Notes

Alleles and Phenotypes

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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

ΔybaW (Keio:JW0433)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8596[3]

ΔybaW729::kan

PMID:16738554[2]

CGSC:103650


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Notes

Genetic Interactions

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Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource Resource Type Source Notes/Reference

JW0433

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCAAACACAAATCAAAGTTCG

Primer 2:CCCTTAACCATCTGCTCCAGCTT

3B6

Kohara Phage

Genobase

PMID:3038334[5]

7E2

Kohara Phage

Genobase

PMID:3038334[5]

19B7

Kohara Phage

Genobase

PMID:3038334[5]

zaj-3054::Tn10

Linked marker

CAG12017 = CGSC7339[3]

est. P1 cotransduction: 87% [6]
Synonyms:zba-3054::Tn10

gsk-3055::Tn10

Linked marker

CAG12154 = CGSC7341[3]

est. P1 cotransduction: 21% [6]
Synonyms:zbb-30-55::TnlO, zba-3055::Tn10

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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b0443

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C0559

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YBAW

EcoCyc (EcoliWiki Page)

ECOCYC:G6244

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945812

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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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 5.2 Kohara, Y et al. (1987) The physical map of the whole E. coli chromosome: application of a new strategy for rapid analysis and sorting of a large genomic library. Cell 50 495-508 PubMed
  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

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