ymjC:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|ymjC}}{{Tab On|Gene|ymjC}}{{Tab|Gene Product(s)|ymjC}}{{Tab|Expression|ymjC}}{{Tab|Evolution|ymjC}}{{Tab|On One Page|ymjC}}{{TabsBottom}}
{{Tab|Quickview|ymjC}}{{Tab On|Gene|ymjC}}{{Tab|Gene Product(s)|ymjC}}{{Tab|Expression|ymjC}}{{Tab|Evolution|ymjC}}{{Tab|On One Page|ymjC}}{{TabsBottom}}
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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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==Nomenclature==
==Nomenclature==
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{{BacktoTop}}
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{|  id="I46a9c4c087365"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''ymjC''  
''ymjC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1323, b4525, JW5960''<ref name='LIB:Riley_2006'/>
''ECK1323, b4525, JW5960''<ref name='LIB:Riley_2006'/>, JW5960''
|-
 
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<!--Nomenclature_notes--></protect>
<!--Nomenclature_notes--></protect>
===Notes===
===Notes===
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==Location(s) and DNA Sequence==
==Location(s) and DNA Sequence==
{{BacktoTop}}
<protect>
<protect>
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="E46a9c4c10ca4d"  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
|-
|-  
|
|
MG1655
MG1655
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29.93 minutes&nbsp;
29.93 minutes&nbsp;
|
|
MG1655: 1388886..1388704<br />{{GBrowseFigureByCoord|1387704|1389886|ecoli|MG1655}}
MG1655: 1388886..1388704<br /><gbrowseImage>
name=NC_000913:1388704..1388886
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10446 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10446 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1387704..1389886 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1387704|1389886|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1388704..1388886&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1388704|1388886|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10446 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10446 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1392576..1392394<br />{{GBrowseFigureByCoord|1391394|1393576|ecoli_W3110|W3110}}  
W3110: 1392576..1392394<br /><gbrowseImage>
name=NC_007779:1392394..1392576
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1391394|1393576|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1392394|1392576|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1391394..1393576 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1392394..1392576&plugin_action=Go FASTA Dump]
DH10B: 1478282..1478100<br /><gbrowseImage>
|-class='sortbottom'
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source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|1477736|1478646|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|1477736|1478646|FASTA Dump}}
 
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<!--Location_notes--></protect>
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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|- {{table_heading_style}}
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!Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!Notes
|-class='sortbottom'
 
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====Notes====
====Notes====
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==Alleles and Phenotypes==
==Alleles and Phenotypes==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9c4c1f0d2c"  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!!CGSC Mutation ID #
!|Allele!!Nt change(s)!!AA change(s)!!Phenotype: Type!!Phenotype: Description!!Reference!!Availability!!Comments
|-class='sortbottom'
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&Delta;ymjC (Keio:JW5960)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
|
 
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="J4e04cc1983702"  class=" tableEdit Genetic_interaction_table dataTable" 
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===Notes===


==Genetic Resources==
==Genetic Resources==
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!|Resource!!Resource Type!!Source!!Notes/Reference
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|
JW5960
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK, cloned as JW1319.5(same sequence)
 
Primer 1:GCCAAAAATGTACTGATTCTTGG
 
Primer 2:CCTCGATCTTGTATCACTTTTTT
|-
|
[[:Category:Kohara_Phage:3H8|3H8]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=259 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:6B4|6B4]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=260 Genobase]
|
PMID:3038334
|-
|
[[ycjM:Gene|zcj-233::Tn10]]
|
Linked marker
|
CAG12028 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39843 CGSC7373]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 48% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zci-233::Tn10
|-
|
[[recT:Gene|recT3061::Tn10]]
|
Linked marker
|
CAG12081 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39818 CGSC7375]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 45% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zcj-3061::Tn10, zda-3061::Tn10
 
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===Notes===
===Notes===
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==Accessions in Other Databases==
==Accessions in Other Databases==
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|- {{table_heading_style}}
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:G0-10446
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=1450258 GeneID:1450258]
|
Escherichia coli str. K-12 substr. MG1655
|-
|
[[RegulonDB]]
|
RegulonDB:ECK120016298
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10446 EcoCyc:G0-10446] 
EchoBASE:EB4394
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[ASAP]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB4394 EchoBASE:EB4394] 
ASAP:ABE-0285046
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
===Notes===
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==Links==
==Links==
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<noinclude><protect>
<noinclude><protect>
==References==
==References==
{{BacktoTop}}
{{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:ymj genes]][[Category:Gene_List:DH10B]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:29, 19 September 2013

{{#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 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

ymjC

Mnemonic
Synonyms

ECK1323, b4525, JW5960[1], JW5960

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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

29.93 minutes 

MG1655: 1388886..1388704
<gbrowseImage> name=NC_000913:1388704..1388886 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1392576..1392394
<gbrowseImage> name=NC_007779:1392394..1392576 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1478282..1478100
<gbrowseImage> name=NC_010473:1478100..1478282 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

ΔymjC (Keio:JW5960)

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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Resource Resource Type Source Notes/Reference

JW5960

Plasmid clone

Shigen

PMID:16769691[3]

Status:Clone OK, cloned as JW1319.5(same sequence)

Primer 1:GCCAAAAATGTACTGATTCTTGG

Primer 2:CCTCGATCTTGTATCACTTTTTT

3H8

Kohara Phage

Genobase

PMID:3038334[4]

6B4

Kohara Phage

Genobase

PMID:3038334[4]

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[5]

est. P1 cotransduction: 48% [6]
Synonyms:zci-233::Tn10

recT3061::Tn10

Linked marker

CAG12081 = CGSC7375[5]

est. P1 cotransduction: 45% [6]
Synonyms:zcj-3061::Tn10, zda-3061::Tn10

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:G0-10446

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:1450258

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120016298

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4394

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0285046

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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References

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  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 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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