rnb: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="W46a9c3d62da90"  class=" tableEdit Gene_nomenclature_table" 
 
|-
!align=left {{table_heading_style}} |Standard name
||
''rnb''
|-
|-
!{{table_heading_style}} |Standard name
!align=left {{table_heading_style}} |Mnemonic
|
||
''rnb''
RNase B
|-
|-
!{{table_heading_style}} |Mnemonic
!align=left {{table_heading_style}} |Synonyms
|
||
''ECK1281, b1286, JW1279''<ref name='LIB:Riley_2006'/>, JW1279''


|-
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!{{table_heading_style}} |Synonyms
|<span class="tableEdit_editLink plainlinks">[{{SERVER}}{{SCRIPTPATH}}?title=Special:TableEdit&id=421aa90e079fa326b6494f812ad13e79.13139.W46a9c3d62da90&page=13139&pagename={{FULLPAGENAMEE}}&type=1&template=Gene_nomenclature_table edit table]</span> ||
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''ECK1281, b1286, JW1279''<ref name='LIB:Riley_2006'/>
|-
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===Notes===
===Notes===
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{|class = 'sortable' {{Prettytable}} id='132618'
{| border="2" cellpadding="4" cellspacing="0" style="margin: 1em 1em 1em 0; border: 1px #aaa solid; border-collapse: collapse;"  id="G46a9c3d6a738b"  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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28.99 minutes&nbsp;
28.99 minutes&nbsp;
|
|
MG1655: 1346936..1345002<br />{{GBrowseFigureByCoord|1344002|1347936|ecoli|MG1655}}
MG1655: 1346936..1345002<br /><gbrowseImage>
name=NC_000913:1345002..1346936
source=MG1655
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11620 EcoCyc]
*[http://biocyc.org/ECOLI/NEW-IMAGE?type=LOCUS-POSITION&chromosome=COLI-K12&object=EG11620 EcoCyc]
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?q=MG1655:1344002..1347936 GBrowse(MG1655)]
{{GBrowseLink|MG1655|NC_000913|1344002|1347936|GBrowse(MG1655)}}
   
   
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli/?plugin=FastaDumper&name=MG1655:1345002..1346936&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|MG1655|NC_000913|1345002|1346936|FASTA Dump}}
*[http://biocyc.org/ECOLI/sequence?object=EG11620 EcoCyc Sequence Dump]  
*[http://biocyc.org/ECOLI/sequence?object=EG11620 EcoCyc Sequence Dump]  
|-
|-
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[[REL606]]
|
 
|
NC_012967: 1347281..1345347<br /><gbrowseImage>
name=NC_012967:1345347..1347281
source=REL606
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|REL606|NC_012967|1345347|1347281|GBrowse (REL606)}}
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{{GBrowseFastaLink|REL606|NC_012967|1345347|1347281|FASTA Dump}}
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[[BW2952]]
|
 
|
NC_012759: 1235851..1237785<br /><gbrowseImage>
name=NC_012759:1235851..1237785
source=BW2952
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|BW2952|NC_012759|1235851|1237785|GBrowse (BW2952)}}
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{{GBrowseFastaLink|BW2952|NC_012759|1235851|1237785|FASTA Dump}}
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W3110
W3110
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&nbsp;
&nbsp;
|
|
W3110: 1350626..1348692<br />{{GBrowseFigureByCoord|1347692|1351626|ecoli_W3110|W3110}}  
W3110: 1350626..1348692<br /><gbrowseImage>
name=NC_007779:1348692..1350626
source=W3110
preset=GeneLocation
</gbrowseImage>
 
|
{{GBrowseLink|W3110|NC_007779|1347692|1351626|GBrowse(W3110)}}
|
{{GBrowseFastaLink|W3110|NC_007779|1348692|1350626|FASTA Dump}}  
|-
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[[DH10B]]
|
 
|
DH10B: 1436332..1434398<br /><gbrowseImage>
name=NC_010473:1434398..1436332
source=DH10B
preset=GeneLocation
</gbrowseImage>
 
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?q=W3110:1347692..1351626 GBrowse(W3110)]
{{GBrowseLink|DH10B|NC_010473|1430530|1440200|GBrowse(DH10B)}}
|
|
*[http://dimer.tamu.edu/cgi-bin/gb/gbrowse/ecoli_W3110/?plugin=FastaDumper&name=W3110:1348692..1350626&plugin_action=Go FASTA Dump]
{{GBrowseFastaLink|DH10B|NC_010473|1430530|1440200|FASTA Dump}}
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===Notes===
===Notes===
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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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|- {{table_heading_style}}
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!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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&Delta;rnb (Keio:JW1279)
&Delta;rnb (Keio:JW1279)
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[[PMID:16738554]]<ref name=PMID:16738554/>
PMID:16738554
|
|
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]
[http://www.shigen.nig.ac.jp/ecoli/strain/keioCollectionQueryAction.do Shigen]<br>[http://cgsc2.biology.yale.edu/Strain.php?ID=107431 CGSC9150]<ref name='LIB:cgsc'/>
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&Delta;rnb::kan
|
deletion
|
 
|
[[Biolog]]:respiration
|
unable to respire [[Carbon sources|Acetate]]
|
PMID:16095938
|
 
|
|-
|
''rnb-464''
|
 
|
 
|
 
|
 
|
 
|
[[cgscmutation:8933|CGSC:8933]]
|
|-
|
''&#916;rnb-723::kan''
|
 
|
 
|
 
|
 
|
PMID:16738554
|
[[cgscmutation:102744|CGSC:102744]]
|
 
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{{Gene_alleles_help}}
 
<protect><!--Alleles_notes--></protect>
<protect><!--Alleles_notes--></protect>
===Notes===
===Notes===


==Genetic Interactions==
{{BacktoTop}}
<protect><!--box uid=bc145ea147f7e36caf09c1bfeed4ee9d.13139.E4e04c2ace4bc6-->
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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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JW1279
JW1279
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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:CCgGCGACCGGGCGCGCAATAAT  
Primer 2:CCgGCGACCGGGCGCGCAATAAT  
|-
|-
|
[[:Category:Kohara_Phage:18B6|18B6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=255 Genobase]
|
PMID:3038334
|-
|
[[:Category:Kohara_Phage:E14F6|E14F6]]
|
Kohara Phage
|
[http://ecoli.aist-nara.ac.jp/GB6/kohara_info.jsp?fword=256 Genobase]
|
PMID:3038334
|-  
|
|
[[trpC:Gene|trpC83::Tn10]]
[[trpC:Gene|trpC83::Tn10]]
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CAG18455 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39837 CGSC7371]<ref name='LIB:cgsc'/>
CAG18455 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39837 CGSC7371]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 35% <ref name='LIB:Nichols_linked_Tn'/> <br />
 
Synonyms:trpB83::Tn10  
Synonyms:trpB83::Tn10  
|-
|-  
|
|
[[ycjM:Gene|zcj-233::Tn10]]
[[ycjM:Gene|zcj-233::Tn10]]
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CAG12028 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39843 CGSC7373]<ref name='LIB:cgsc'/>
CAG12028 = [http://cgsc2.biology.yale.edu/Strain.php?ID=39843 CGSC7373]<ref name='LIB:cgsc'/>
|
|
est. P1 cotransduction: 41% <ref name='LIB:Nichols_linked_Tn'/>
est. P1 cotransduction: 41% <ref name='LIB:Nichols_linked_Tn'/> <br />
Synonyms:zci-233::Tn10


Synonyms:zci-233::Tn10
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===Notes===
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!Database!!Accession!!Notes
!|Database!!Accession!!Notes
|-
|-  
|
[http://ecocyc.org EcoCyc] ([[EcoCyc|EcoliWiki Page]])
|
[http://biocyc.org/ECOLI/NEW-IMAGE?type=NIL&object=EG11620 EcoCyc:EG11620] 
|
|-
|
|
[http://www.ecoli-york.org EchoBASE] ([[EchoBASE|EcoliWiki Page]])
[[EcoCyc]]
|
|
[http://www.york.ac.uk/res/thomas/Gene.cfm?recordID=EB1577 EchoBASE:EB1577] 
EcoCyc:EG11620
|
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''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://chase.ou.edu/oubcf/index.php EcoliGenExpDB] ([[EcoliGenExpDB|EcoliWiki Page]])
[[EcoGene]]
|
|
[http://chase.ou.edu/macro/searchlink.php?bnum=b1286 EcoliGenExpDB:b1286] 
EcoGene:EG11620
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://BioCyc.org/ECOL199310/ ECOL199310CYC] ([[ECOL199310CYC|EcoliWiki Page]])
[[RegulonDB]]
|
|
[http://BioCyc.org/ECOL199310/new-image?object=C1757 ECOL199310CYC:C1757] 
RegulonDB:ECK120001568
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[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=EG11620 EcoGene:EG11620]
[http://www.ncbi.nlm.nih.gov/gene?term=945864 GeneID:945864]
|
|
Escherichia coli str. K-12 substr. MG1655
|-
|-  
|
|
[http://BioCyc.org/ECOO157/ ECOO157CYC] ([[ECOO157CYC|EcoliWiki Page]])
[[EchoBASE]]
|
|
[http://BioCyc.org/ECOO157/new-image?object=RNB ECOO157CYC:RNB] 
EchoBASE:EB1577
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
|-
|-  
|
|
[http://cgsc.biology.yale.edu CGSC] ([[CGSC|EcoliWiki Page]])
[[ASAP]]
|
|
[http://cgsc.biology.yale.edu/cgi-bin/sybgw/cgsc/Site/272 CGSC:272] 
ASAP:ABE-0004320
|
|
''Escherichia coli'' str. K-12 substr. [[:Category:Strain:MG1655|MG1655]]
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===Notes===
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===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:rnb genes]][[Category:Gene_List:DH10B]][[Category:Gene_List:REL606]]
[[Category:Gene_List:BW2952]]

Latest revision as of 20:30, 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

rnb

Mnemonic

RNase B

Synonyms

ECK1281, b1286, JW1279[1], JW1279

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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

28.99 minutes 

MG1655: 1346936..1345002
<gbrowseImage> name=NC_000913:1345002..1346936 source=MG1655 preset=GeneLocation </gbrowseImage>

REL606

NC_012967: 1347281..1345347
<gbrowseImage> name=NC_012967:1345347..1347281 source=REL606 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1235851..1237785
<gbrowseImage> name=NC_012759:1235851..1237785 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1350626..1348692
<gbrowseImage> name=NC_007779:1348692..1350626 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 1436332..1434398
<gbrowseImage> name=NC_010473:1434398..1436332 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

Δrnb (Keio:JW1279)

deletion

deletion

PMID:16738554[2]

Shigen
CGSC9150[3]

Δrnb::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938[4]

rnb-464

CGSC:8933

Δrnb-723::kan

PMID:16738554[2]

CGSC:102744


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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

JW1279

Plasmid clone

Shigen

PMID:16769691[5]

Status:Clone OK

Primer 1:GCCTTTCAGGACAACCCGCTGCT

Primer 2:CCgGCGACCGGGCGCGCAATAAT

18B6

Kohara Phage

Genobase

PMID:3038334[6]

E14F6

Kohara Phage

Genobase

PMID:3038334[6]

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[3]

est. P1 cotransduction: 35% [7]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[3]

est. P1 cotransduction: 41% [7]
Synonyms:zci-233::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:EG11620

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11620

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001568

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:945864

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1577

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004320

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. ↑ Ito, M et al. (2005) Functional analysis of 1440 Escherichia coli genes using the combination of knock-out library and phenotype microarrays. Metab. Eng. 7 318-27 PubMed
  5. ↑ 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
  6. ↑ 6.0 6.1 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
  7. ↑ 7.0 7.1 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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