rlmD:Gene: Difference between revisions

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<noinclude>{{TabsTop}}  
<noinclude>{{TabsTop}}  
{{Tab|Quickview|rumB}}{{Tab On|Gene|rumB}}{{Tab|Gene Product(s)|rumB}}{{Tab|Expression|rumB}}{{Tab|Evolution|rumB}}{{Tab|On One Page|rumB}}{{TabsBottom}}
{{Tab|Quickview|rlmD}}{{Tab On|Gene|rlmD}}{{Tab|Gene Product(s)|rlmD}}{{Tab|Expression|rlmD}}{{Tab|Evolution|rlmD}}{{Tab|On One Page|rlmD}}{{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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{|   id="O46a9ba4e7a1c0"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''rlmD''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''rumB''
RNA uridine methlytransferase
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''rumB, ECK0850, b0859, JW0843, ybjF''<ref name='LIB:Riley_2006'/>, ybjF''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.12277.O46a9ba4e7a1c0&page=12277&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK0850, b0859, JW0843, ybjF''<ref name='LIB:Riley_2006'/>
|-
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===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="W46a9ba4ef20b6"  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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19.35 minutes&nbsp;
19.35 minutes&nbsp;
|
|
MG1655: 897741..898868<br />{{GBrowseFigureByCoord|896741|899868|ecoli|MG1655}}
MG1655: 897741..898868<br /><gbrowseImage>
name=NC_000913:897741..898868
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6449 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=G6449 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:896741..899868 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|896741|899868|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:897741..898868&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|897741|898868|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=G6449 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=G6449 EcoCyc Sequence Dump]  
|-
|-
|
[[REL606]]
|
 
|
NC_012967: 915225..916352<br /><gbrowseImage>
name=NC_012967:915225..916352
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|915225|916352|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|915225|916352|FASTA Dump}}
|-
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[[BW2952]]
|
 
|
NC_012759: 800709..801836<br /><gbrowseImage>
name=NC_012759:800709..801836
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|800709|801836|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|800709|801836|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
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W3110: 898940..900067<br />{{GBrowseFigureByCoord|897940|901067|ecoli_W3110|W3110}}  
W3110: 898940..900067<br /><gbrowseImage>
name=NC_007779:898940..900067
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|897940|901067|GBrowse(W3110)}}
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{{GBrowseFastaLink|W3110|NC_007779|898940|900067|FASTA Dump}}  
|-
|
[[DH10B]]
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:897940..901067 GBrowse(W3110)]
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:898940..900067&plugin_action=Go FASTA Dump]
DH10B: 951669..952796<br /><gbrowseImage>
|-class='sortbottom'
name=NC_010473:951669..952796
|[{{SERVER}}/colipedia/index.php/Special:TableEdit?id=421aa90e079fa326b6494f812ad13e79..D469f9d3e10738&page=&pagename={{FULLPAGENAMEE}} edit table] || || || ||
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|DH10B|NC_010473|949415|955050|GBrowse(DH10B)}}
|
{{GBrowseFastaLink|DH10B|NC_010473|949415|955050|FASTA Dump}}
 
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===Notes===
===Notes===
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==Sequence Features==
==Sequence Features==
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{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="V46a9ba4f9b894"  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
|-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="A46a9ba4fdba88"  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;rumB (Keio:JW0843)
|
deletion
|
deletion
|
 
|
 
|
PMID:16738554
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107160 CGSC8879]<ref name='LIB:cgsc'/>
|
|-
|
''&#916;rumB760::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102850|CGSC:102850]]
|
 
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<protect><!--Alleles_notes--></protect>
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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="T4e04c29515024"  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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!Resource!!Resource Type!!Source!!Notes/Reference
!|Resource!!Resource Type!!Source!!Notes/Reference
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|
JW0843
|
Plasmid clone
|
[http://www.shigen.nig.ac.jp/ecoli/strain/askaCloneQueryAction.do?strainTypeId=9 Shigen]
|
PMID:16769691
 
Status:Clone OK
 
Primer 1:GCCCAGTGCGCACTTTACGACGC
 
Primer 2:CCTTGCTTCACCAGCAGCGTCAG
|-
|
zbh-29::Tn10
|
Linked marker
|
CAG18493 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39400 CGSC7353]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 1% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbi-29::Tn10
|-
|
zca-1230::Tn10
|
Linked marker
|
CAG18478 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39407 CGSC7356]<ref name='LIB:cgsc'/>
|
est. P1 cotransduction: 11% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zbj-1230::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
|-
|-  
|
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=G6449 EcoCyc:G6449] 
EcoCyc:EG11247
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB3201 EchoBASE:EB3201] 
EcoGene:EG11247
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b0859 EcoliGenExpDB:b0859] 
RegulonDB:ECK120001223
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])  
[http://www.ncbi.nlm.nih.gov/gene NCBI] ([[NCBI|EcoliWiki Page]])
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C0992 ECOL199310CYC:C0992]
[http://www.ncbi.nlm.nih.gov/gene?term=947260 GeneID:947260]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://ecogene.org EcoGene] ([[EcoGene|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://ecogene.org/geneinfo.php?eg_id=EG13427 EcoGene:EG13427] 
EchoBASE:EB1228
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=YBJF ECOO157CYC:YBJF] 
ASAP:ABE-0009127
|
|
''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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==References==
==References==
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<references/>
<references />
__NOTOC__
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===Categories===
[[Category:Gene List:MG1655]]
[[Category:Gene List:W3110]]
[[Category:Genes in the Keio knockout collection]]
[[Category:Genes in the ASKA clone collection]]
[[Category:rum genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:33, 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

rlmD

Mnemonic

RNA uridine methlytransferase

Synonyms

rumB, ECK0850, b0859, JW0843, ybjF[1], ybjF

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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

19.35 minutes 

MG1655: 897741..898868
<gbrowseImage> name=NC_000913:897741..898868 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 915225..916352
<gbrowseImage> name=NC_012967:915225..916352 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 800709..801836
<gbrowseImage> name=NC_012759:800709..801836 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 898940..900067
<gbrowseImage> name=NC_007779:898940..900067 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 951669..952796
<gbrowseImage> name=NC_010473:951669..952796 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

ΔrumB (Keio:JW0843)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC8879[3]

ΔrumB760::kan

PMID:16738554[2]

CGSC:102850


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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

JW0843

Plasmid clone

Shigen

PMID:16769691[4]

Status:Clone OK

Primer 1:GCCCAGTGCGCACTTTACGACGC

Primer 2:CCTTGCTTCACCAGCAGCGTCAG

zbh-29::Tn10

Linked marker

CAG18493 = CGSC7353[3]

est. P1 cotransduction: 1% [5]
Synonyms:zbi-29::Tn10

zca-1230::Tn10

Linked marker

CAG18478 = CGSC7356[3]

est. P1 cotransduction: 11% [5]
Synonyms:zbj-1230::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:EG11247

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11247

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001223

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:947260

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1228

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0009127

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 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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