yncM:Gene: Difference between revisions

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|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Nomenclature |Nomenclature]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Location(s) and DNA Sequence|Location(s) and DNA Sequence]]
|{{Sub}}[[#Sequence Features|Sequence Features]]
|{{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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|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|{{Sub}}[[Talk:{{PAGENAMEE}}| Suggestions]]
|}
|}
[[Category:Gene List:MG1655]][[Category:Gene List:W3110]][[Category:Genes in the Keio knockout collection]][[Category:Genes in the ASKA clone collection]]
</noinclude><protect>
</noinclude><protect>
==Nomenclature==
==Nomenclature==
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{|  id="N46a9c779511e2"  class=" tableEdit Gene_nomenclature_table" 
 
|-
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!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yncM''  
''yncM''
|-
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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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''ECK1453, b1459, JW5237''<ref name='LIB:Riley_2006'/>
''ECK1453, b1459, JW5237''<ref name='LIB:Riley_2006'/>
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="M46a9c779cc0b2"  class=" tableEdit Gene_location_table" 
|- {{table_heading_style}}
|- {{table_heading_style}}
!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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32.96 minutes&nbsp;
32.96 minutes&nbsp;
|
|
MG1655: 1529400..1529600<br />{{GBrowseFigureByCoord|1528400|1530600|ecoli|MG1655}}
MG1655: 1529400..1529600<br /><gbrowseImage>
name=NC_000913:1529400..1529600
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6768 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6768 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1528400..1530600 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1528400|1530600|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1529400..1529600&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1529400|1529600|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6768 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6768 EcoCyc Sequence Dump]  
|-
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 1533090..1533290<br />{{GBrowseFigureByCoord|1532090|1534290|ecoli_W3110|W3110}}
W3110: 1533090..1533290<br /><gbrowseImage>
name=NC_007779:1533090..1533290
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1532090..1534290 GBrowse(W3110)]
{{GBrowseLink|W3110|NC_007779|1532090|1534290|GBrowse(W3110)}}
|
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*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1533090..1533290&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|1533090|1533290|FASTA Dump}}
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===Notes===
===Notes===
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="U46a9c77a7b89d"  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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====Notes====
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="A46a9c77abdf10"  class=" tableEdit Gene_allele_table dataTable" 
|- {{table_heading_style}}
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!Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-
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&Delta;yncM (Keio:JW5237)
&Delta;yncM (Keio:JW5237)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
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<protect><!--Alleles_notes--></protect>
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===Notes===
===Notes===


==Genetic Interactions==
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<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13483.X4e04cc33a9cd1-->
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="X4e04cc33a9cd1"  class=" tableEdit Genetic_interaction_table dataTable" 
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!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
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<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J46a9c77b6d445"  class=" tableEdit Gene_resource_table" 
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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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JW5237
JW5237
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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:CCGGCTGCGTTTCCTCTTCTTAT  
Primer 2:CCGGCTGCGTTTCCTCTTCTTAT  
|-
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[[:Category:Kohara_Phage:8B7|8B7]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=274 Genobase]
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PMID:3038334
|-
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[[:Category:Kohara_Phage:6D4|6D4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=275 Genobase]
|
PMID:3038334
|-
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[[:Category:Kohara_Phage:1G4|1G4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=276 Genobase]
|
PMID:3038334
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[[trg:Gene|trg-2::Tn10]]
[[trg:Gene|trg-2::Tn10]]
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est. P1 cotransduction: 24% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 24% <ref name='LIB:Nichols_linked_Tn'/>  
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[[yddE:Gene|zdd-235::Tn10]]
[[yddE:Gene|zdd-235::Tn10]]
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CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
CAG18461 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39848 CGSC7378]<ref name='LIB:cgsc'/>
|
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est. P1 cotransduction: 81% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 81% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdc-235::Tn10


Synonyms:zdc-235::Tn10
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!Database!!Accession!!Notes
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[[EcoCyc]]
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EcoCyc:G6768
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoGene]]
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[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6768 EcoCyc:G6768] 
EcoGene:EG14258
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[RegulonDB]]
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[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4346 EchoBASE:EB4346] 
RegulonDB:ECK120003357
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EchoBASE]]
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[http://chase.ou.edu/macro/searchlink.php?bnum=b1459 EcoliGenExpDB:b1459] 
EchoBASE:EB4346
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
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[http://BioCyc.org/ECOO157/new-image?object=Z0854 ECOO157CYC:Z0854] 
ASAP:ABE-0004868
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
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{{BacktoTop}}
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{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:ync genes]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:29, 19 September 2013

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Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Nomenclature Location(s) and DNA Sequence Sequence Features 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

yncM

Mnemonic
Synonyms

ECK1453, b1459, JW5237[1]

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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

32.96 minutes 

MG1655: 1529400..1529600
<gbrowseImage> name=NC_000913:1529400..1529600 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1533090..1533290
<gbrowseImage> name=NC_007779:1533090..1533290 source=W3110 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

ΔyncM (Keio:JW5237)

deletion

deletion

PMID:16738554[2]

Shigen


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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

JW5237

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK

Primer 1:GCCTCATTCAGGCAGAAGAAAGA

Primer 2:CCGGCTGCGTTTCCTCTTCTTAT

8B7

Kohara Phage

Genobase

PMID:3038334[4]

6D4

Kohara Phage

Genobase

PMID:3038334[4]

1G4

Kohara Phage

Genobase

PMID:3038334[4]

trg-2::Tn10

Linked marker

CAG12026 = CGSC7376[5]

est. P1 cotransduction: 24% [6]

zdd-235::Tn10

Linked marker

CAG18461 = CGSC7378[5]

est. P1 cotransduction: 81% [6]
Synonyms:zdc-235::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

EcoCyc

EcoCyc:G6768

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG14258

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120003357

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4346

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004868

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. ↑ 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. ↑ 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 4.2 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
  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).

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