rlmA:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|rrmA}}{{Tab On|Gene|rrmA}}{{Tab|Gene Product(s)|rrmA}}{{Tab|Expression|rrmA}}{{Tab|Evolution|rrmA}}{{Tab|On One Page|rrmA}}{{TabsBottom}}
{{Tab|Quickview|rlmA}}{{Tab On|Gene|rlmA}}{{Tab|Gene Product(s)|rlmA}}{{Tab|Expression|rlmA}}{{Tab|Evolution|rlmA}}{{Tab|On One Page|rlmA}}{{TabsBottom}}
{|
{|
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|- style="background-color:white; border:solid 2px #CCFFFF; text-align:center; white-space: nowrap;"  
|{{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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****************************************************************************************** -->{{Gene_nomenclature_help}}
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{|border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  
{|   id="L46a9cfb675b34" class=" tableEdit Gene_nomenclature_table"


|-
|-
!align=left {{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Standard name
||
||
''rrmA''  
''rlmA''
|-
|-
!align=left {{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Mnemonic
||
||
 
rRNA large-subunit methylation
|-
|-
!align=left {{table_heading_style}} |Synonyms
!align=left {{table_heading_style}} |Synonyms
||
||
''ECK1820, b1822, JW1811, yebH, RlmAI''<ref name='LIB:Riley_2006'/>
''ECK1820, b1822, JW1811, yebH, RlmAI'', rrmA<ref name='LIB:Riley_2006'/>, rrmA''


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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="S46a9cfb6f1949"  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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41.04 minutes&nbsp;
41.04 minutes&nbsp;
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|
MG1655: 1905084..1904275<br />{{GBrowseFigureByCoord|1903275|1906084|ecoli|MG1655}}
MG1655: 1905084..1904275<br /><gbrowseImage>
name=NC_000913:1904275..1905084
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12207 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG12207 EcoCyc]
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{{GBrowseFastaLink|ecoli|NC_000913|1904275|1905084|FASTA Dump}}
{{GBrowseFastaLink|ecoli|NC_000913|1904275|1905084|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG12207 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG12207 EcoCyc Sequence Dump]  
|-
|
[[REL606]]
|
|
NC_012967: 1884830..1885639<br /><gbrowseImage>
name=NC_012967:1884830..1885639
source=REL606
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|REL606|NC_012967|1884830|1885639|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|1884830|1885639|FASTA Dump}}
|-
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[[BW2952]]
|
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NC_012759: 1796334..1797143<br /><gbrowseImage>
name=NC_012759:1796334..1797143
source=BW2952
preset=GeneLocation
</gbrowseImage>
|
{{GBrowseLink|BW2952|012759|1796334|NC_1797143|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|012759|1796334|NC_1797143|FASTA Dump}}
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&nbsp;
&nbsp;
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W3110: 1908774..1907965<br />{{GBrowseFigureByCoord|1906965|1909774|ecoli_W3110|W3110}}
W3110: 1908774..1907965<br /><gbrowseImage>
name=NC_007779:1907965..1908774
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
|
{{GBrowseLink|ecoli_W3110|AC_000091|1906965|1909774|GBrowse(W3110)}}  
{{GBrowseLink|ecoli_W3110|NC_007779|1906965|1909774|GBrowse(W3110)}}  
|
{{GBrowseFastaLink|ecoli_W3110|NC_007779|1907965|1908774|FASTA Dump}}
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[[DH10B]]
|
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{{GBrowseFastaLink|ecoli_W3110|AC_000091|1907965|1908774|FASTA Dump}}


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DH10B: 1995655..1994846<br /><gbrowseImage>
name=NC_010473:1994846..1995655
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|ecoli_DH10B|NC_010473|1993228|1997273|GBrowse(DH10B)}}
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{{GBrowseFastaLink|ecoli_DH10B|NC_010473|1993228|1997273|FASTA Dump}}
 
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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;"   
{|   id="V46a9cfb7a4f0f" class=" tableEdit Gene_sequence_features_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|Feature type!!Location!!Description
!|Feature Type!!Strain!!Genomic Location!!Evidence!!Reference!!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="A46a9cfb7e8b91" 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
|
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[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107795 CGSC9514]<ref name='LIB:cgsc'/>  
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107795 CGSC9514]<ref name='LIB:cgsc'/>  
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|[[PMID:16738554]]<ref name=PMID:16738554/>
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PMID:16738554
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[[cgscmutation:102802|CGSC:102802]]
[[cgscmutation:102802|CGSC:102802]]
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===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14215.R4e04c291dd398-->
<!--
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*
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="R4e04c291dd398"  class=" tableEdit Genetic_interaction_table dataTable" 
|- {{table_heading_style}}
!|Interactor!!Interaction!!Allele!!Score(s)!!Reference(s)!!Accessions!!Notes
|- class="tableEdit_footer"
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<!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.14215.R4e04c291dd398--></protect>
<!-- Genetic Interacdtions Notes -->
===Notes===


==Genetic Resources==
==Genetic Resources==
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{|   id="U46a9cfb89b5eb" class=" tableEdit Gene_resource_table"   
|- {{table_heading_style}}
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!|Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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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]
|[[PMID:16769691]]<ref name=PMID:16769691/>
|
PMID:16769691


Status:Clone OK
Status:Clone OK
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Primer 2:CCATAAGAACGCTGCCAGAGGTG  
Primer 2:CCATAAGAACGCTGCCAGAGGTG  
|-
|
[[:Category:Kohara_Phage:15D5|15D5]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=335 Genobase]
|
PMID:3038334
|-  
|-  
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CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
CAG18465 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39973 CGSC7388]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/>nnSynonyms:zdj-225::Tn10  
est. P1 cotransduction: 25% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zdj-225::Tn10  
|-  
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est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>  
est. P1 cotransduction: 38% <ref name='LIB:Nichols_linked_Tn'/>  


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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="J46a9cfb93822e"  class=" tableEdit Gene_accessions_table"   
|- {{table_heading_style}}
|- {{table_heading_style}}
!|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=EG12207 EcoCyc:EG12207]
[http://chase.ou.edu/macro/searchlink.php?bnum=b1822 EcoliGenExpDB:b1822]
|
|
   
   
|-  
|-  
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[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=EB2122 EchoBASE:EB2122]
[http://BioCyc.org/ECOL199310/new-image?object=C2229 ECOL199310CYC:C2229]
|
|
   
   
|-  
|-  
|
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[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])  
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])  
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1822 EcoliGenExpDB:b1822]
[http://BioCyc.org/ECOO157/new-image?object=YEBH ECOO157CYC:YEBH]
|
|
   
   
|-  
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C2229 ECOL199310CYC:C2229]
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG12207 ECOCYC:EG12207]
|
|
Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
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[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=EG12207 EcoGene:EG12207]
[http://www.ncbi.nlm.nih.gov/gene?term=946340 GeneID:946340]
|
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Escherichia coli str. K-12 substr. MG1655
|-  
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YEBH ECOO157CYC:YEBH]
RegulonDB:
|
|-
|
[https://asap.ahabs.wisc.edu/asap/logon.php ASAP] ([[ASAP|EcoliWikiPage]])
|
[http://asap.ahabs.wisc.edu/asap/feature_info.php?LocationID=WIS&FeatureID=0006067&formSubmitReturn=1 ASAP:ABE-0006067]
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]


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!|Name!!URL!!Comments


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==References==
==References==
{{BacktoTop}}
{{BacktoTop}}
 
{{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 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:rrm genes]]
[[Category:rrm genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:rlm genes]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:39, 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

rlmA

Mnemonic

rRNA large-subunit methylation

Synonyms

ECK1820, b1822, JW1811, yebH, RlmAI, rrmA[1], rrmA

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

41.04 minutes 

MG1655: 1905084..1904275
<gbrowseImage> name=NC_000913:1904275..1905084 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1884830..1885639
<gbrowseImage> name=NC_012967:1884830..1885639 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1796334..1797143
<gbrowseImage> name=NC_012759:1796334..1797143 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1908774..1907965
<gbrowseImage> name=NC_007779:1907965..1908774 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1995655..1994846
<gbrowseImage> name=NC_010473:1994846..1995655 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

ΔrrmA (Keio:JW1811)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9514[3]

ΔrrmA746::kan

PMID:16738554[2]

CGSC:102802


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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

JW1811

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCTCTTTTTCCTGTCCACTTTG

Primer 2:CCATAAGAACGCTGCCAGAGGTG

15D5

Kohara Phage

Genobase

PMID:3038334[5]

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[3]

est. P1 cotransduction: 25% [6]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[3]

est. P1 cotransduction: 38% [6]

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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:b1822

ECOL199310CYC (EcoliWiki Page)

ECOL199310CYC:C2229

ECOO157CYC (EcoliWiki Page)

ECOO157CYC:YEBH

EcoCyc (EcoliWiki Page)

ECOCYC:EG12207

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:946340

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. ↑ 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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