yrhC: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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{|{{Prettytable}}
{|  id="K46a9f70ed2ebe"  class=" tableEdit Gene_nomenclature_table" 
 
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
|
||
''yrhC''  
''yrhC''
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
|
||


|-
|-
!{{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK3468, b4552, JW5678''<ref name='LIB:Riley_2006'/>
''ECK3468, b4552, JW5678''<ref name='LIB:Riley_2006'/>, JW5678''
|-
 
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='145737'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="F46a9f70f60324"  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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78.06 minutes, 78.06 minutes&nbsp;
78.06 minutes, 78.06 minutes&nbsp;
|
|
MG1655: 3621910..3622155<br />{{GBrowseFigureByCoord|3620910|3623155|ecoli|MG1655}}
MG1655: 3621910..3622155<br /><gbrowseImage>
name=NC_000913:3621910..3622155
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10563 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G0-10563 EcoCyc]
{{GBrowseLink|ecoli|NC_000913|3620910|3623155|GBrowse(MG1655)}}
{{GBrowseLink|MG1655|NC_000913|3620910|3623155|GBrowse(MG1655)}}
   
   
|
|
{{GBrowseFastaLink|ecoli|NC_000913|3621910|3622155|FASTA Dump}}
{{GBrowseFastaLink|MG1655|NC_000913|3621910|3622155|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G0-10563 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G0-10563 EcoCyc Sequence Dump]  
|-
|-  
|
|
W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 4016528..4016283<br />{{GBrowseFigureByCoord|4015283|4017528|ecoli_W3110|W3110}}
W3110: 4016528..4016283<br /><gbrowseImage>
name=NC_007779:4016283..4016528
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|4015283|4017528|GBrowse(W3110)}}  
{{GBrowseLink|W3110|NC_007779|4015283|4017528|GBrowse(W3110)}}  
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:4016283..4016528&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|W3110|NC_007779|4016283|4016528|FASTA Dump}}
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[[DH10B]]
|
 
|
DH10B: 3719655..3719900<br /><gbrowseImage>
name=NC_010473:3719655..3719900
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|3719165|3720390|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|3719165|3720390|FASTA Dump}}
 
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===Notes===
===Notes===
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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}}
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;" id="Y46a9f71070973"  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=109796 CGSC11515]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=109796 CGSC11515]<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:106060|CGSC:106060]]
[[cgscmutation:106060|CGSC:106060]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
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===Notes===


==Genetic Resources==
==Genetic Resources==
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JW5678
JW5678
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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:CCTATTTGCCCGAGTATAAATGC  
Primer 2:CCTATTTGCCCGAGTATAAATGC  
|-
|-
|
[[:Category:Kohara_Phage:10D10|10D10]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=610 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:5F2|5F2]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=611 Genobase]
|
PMID:3038334
|-  
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zhg-50::Tn10
zhg-50::Tn10
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CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
CAG18450 = [http://cgsc2.biology.yale.edu/Strain.php?ID=37863 CGSC7450]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 30% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
Synonyms:zhf-50::Tn10, zhf-5::Tn10  
|-
|-  
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zic-4901::Tn10
zic-4901::Tn10
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est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: % <ref name='LIB:Nichols_linked_Tn'/>  
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-
|
[[EcoCyc]]
|
EcoCyc:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
[http://www.ncbi.nlm.nih.gov/gene?term=1450291 GeneID:1450291]
|
Escherichia coli str. K-12 substr. MG1655
|-
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[[RegulonDB]]
|
RegulonDB:ECK120026454
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
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[[EchoBASE]]
|
EchoBASE:
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-  
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[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[ASAP]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G0-10563 EcoCyc:G0-10563] 
ASAP:
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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<noinclude><protect>
<noinclude><protect>
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{{BacktoTop}}
{{BacktoTop}}
{{RefHelp}}
{{RefHelp}}
<references/>
<references />
__NOTOC__
__NOTOC__
</protect></noinclude>
===Categories===
===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:MG1655]]
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[[Category:Genes in the ASKA clone collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:yrh genes]]
[[Category:yrh genes]]
[[Category:y genes]]
[[Category:y genes]]

Latest revision as of 20:48, 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

[back to top]


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

Standard name

yrhC

Mnemonic
Synonyms

ECK3468, b4552, JW5678[1], JW5678

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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

78.06 minutes, 78.06 minutes 

MG1655: 3621910..3622155
<gbrowseImage> name=NC_000913:3621910..3622155 source=MG1655 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 4016528..4016283
<gbrowseImage> name=NC_007779:4016283..4016528 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 3719655..3719900
<gbrowseImage> name=NC_010473:3719655..3719900 source=DH10B preset=GeneLocation </gbrowseImage>

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Notes

Sequence Features

[back to top]


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

ΔyrhC (Keio:JW5678)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC11515[3]

ΔyrhC738::kan

PMID:16738554[2]

CGSC:106060


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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

[back to top]


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

Resource Resource Type Source Notes/Reference

JW5678

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCAAATACATACCAGAAAAG

Primer 2:CCTATTTGCCCGAGTATAAATGC

10D10

Kohara Phage

Genobase

PMID:3038334[5]

5F2

Kohara Phage

Genobase

PMID:3038334[5]

zhg-50::Tn10

Linked marker

CAG18450 = CGSC7450[3]

est. P1 cotransduction: 30% [6]
Synonyms:zhf-50::Tn10, zhf-5::Tn10

zic-4901::Tn10

Linked marker

CAG18492 = CGSC7457[3]

est. P1 cotransduction: % [6]

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Notes

Accessions in Other Databases

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Database Accession Notes

EcoCyc

EcoCyc:

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:1450291

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120026454

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:

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. ↑ 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 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).

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