rnb:On One Page

From EcoliWiki
Jump to: navigation, search

{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Quickview   Gene   Gene Product(s)   Expression   Evolution   On One Page    
Quickview | Gene | Product(s) | Expression| Evolution | References |

Quickview

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

<protect>

Standard Name

rnb

Gene Synonym(s)

ECK1281, b1286, JW1279[1], JW1279

Product Desc.

RNase II, mRNA degradation[2]; ribonuclease II[3]

RNase II; mRNA degradation[4]

Product Synonyms(s)

ribonuclease II[1], B1286[2][1], Rnb[2][1], RNase II[3][1] , ECK1281, JW1279, b1286

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): rnb[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png proteindisplay.png   pubmed.jpg   textpresso.jpg  

edit table

</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

[back to top]





Gene

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css> <protect>

Nomenclature

[back to top]


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

edit table

</protect>

Notes

Location(s) and DNA Sequence

[back to top]


<protect> 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>

edit table

</protect>

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
edit table

<protect></protect>

Notes

Alleles and Phenotypes

[back to top]


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

Shigen
CGSC9150[5]

Δrnb::kan

deletion

Biolog:respiration

unable to respire Acetate

PMID:16095938

rnb-464

CGSC:8933

Δrnb-723::kan

PMID:16738554

CGSC:102744


edit table

<protect></protect>

Notes

Genetic Interactions

[back to top]


<protect>

Interactor Interaction Allele Score(s) Reference(s) Accessions Notes
edit table

</protect>

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

JW1279

Plasmid clone

Shigen

PMID:16769691

Status:Clone OK

Primer 1:GCCTTTCAGGACAACCCGCTGCT

Primer 2:CCgGCGACCGGGCGCGCAATAAT

18B6

Kohara Phage

Genobase

PMID:3038334

E14F6

Kohara Phage

Genobase

PMID:3038334

trpC83::Tn10

Linked marker

CAG18455 = CGSC7371[5]

est. P1 cotransduction: 35% [6]
Synonyms:trpB83::Tn10

zcj-233::Tn10

Linked marker

CAG12028 = CGSC7373[5]

est. P1 cotransduction: 41% [6]
Synonyms:zci-233::Tn10

edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


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

edit table

<protect></protect>

Notes

Links

[back to top]



Product(s)

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name

Rnb

Synonyms

ribonuclease II[1], B1286[2][1], Rnb[2][1], RNase II[3][1] , ECK1281, JW1279, b1286

Product description

RNase II, mRNA degradation[2]; ribonuclease II[3]

RNase II; mRNA degradation[4]

EC number (for enzymes)
edit table

<protect></protect>

Notes

Function

[back to top]


<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier GO ID GO term name Reference Evidence Code with/from Aspect Notes Status

GO:0003676

nucleic acid binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011129

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001900

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR003029

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011804

F

Seeded from EcoCyc (v14.0)

complete

GO:0003723

RNA binding

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0694

F

Seeded from EcoCyc (v14.0)

complete

GO:0004518

nuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0540

F

Seeded from EcoCyc (v14.0)

complete

GO:0004527

exonuclease activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0269

F

Seeded from EcoCyc (v14.0)

complete

GO:0004540

ribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR001900

F

Seeded from EcoCyc (v14.0)

complete

GO:0004540

ribonuclease activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

F

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01036

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0963

C

Seeded from EcoCyc (v14.0)

complete

GO:0005737

cytoplasm

GO_REF:0000023

IEA: Inferred from Electronic Annotation

SP_SL:SL-0086

C

Seeded from EcoCyc (v14.0)

complete

GO:0006401

RNA catabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011804

P

Seeded from EcoCyc (v14.0)

complete

GO:0006402

mRNA catabolic process

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01036

P

Seeded from EcoCyc (v14.0)

complete

GO:0008859

exoribonuclease II activity

GOA:hamap
GO_REF:0000020

IEA: Inferred from Electronic Annotation

HAMAP:MF_01036

F

Seeded from EcoCyc (v14.0)

complete

GO:0008859

exoribonuclease II activity

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR011804

F

Seeded from EcoCyc (v14.0)

complete

GO:0008859

exoribonuclease II activity

GOA:spec
GO_REF:0000003

IEA: Inferred from Electronic Annotation

EC:3.1.13.1

F

Seeded from EcoCyc (v14.0)

complete

GO:0016070

RNA metabolic process

GOA:interpro
GO_REF:0000002

IEA: Inferred from Electronic Annotation

InterPro:IPR004476

P

Seeded from EcoCyc (v14.0)

complete

GO:0016787

hydrolase activity

GOA:spkw
SP_KW:GO_REF:0000004

IEA: Inferred from Electronic Annotation

SP_KW:KW-0378

F

Seeded from EcoCyc (v14.0)

complete

edit table

Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type Partner Notes References Evidence

Protein

rnc

PMID:15690043

Experiment(s):EBI-888391

Protein

rpsE

PMID:15690043

Experiment(s):EBI-888410

Protein

thiC

PMID:16606699

Experiment(s):EBI-1139475

Protein

acs

PMID:16606699

Experiment(s):EBI-1139475

Protein

nadE

PMID:16606699

Experiment(s):EBI-1139475

Protein

htpG

PMID:16606699

Experiment(s):EBI-1139475

Protein

fusA

PMID:16606699

Experiment(s):EBI-1139475

Protein

ileS

PMID:16606699

Experiment(s):EBI-1139475
edit table

</protect>

Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment Description Evidence Reference/Source Notes
edit table

<protect></protect>

Notes

Structure and Physical Properties

[back to top]


<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence

at EcoCyc 

MFQDNPLLAQ LKQQLHSQTP RAEGVVKATE KGFGFLEVDA QKSYFIPPPQ MKKVMHGDRI
IAVIHSEKER ESAEPEELVE PFLTRFVGKV QGKNDRLAIV PDHPLLKDAI PCRAARGLNH
EFKEGDWAVA EMRRHPLKGD RSFYAELTQY ITFGDDHFVP WWVTLARHNL EKEAPDGVAT
EMLDEGLVRE DLTALDFVTI DSASTEDMDD ALFAKALPDD KLQLIVAIAD PTAWIAEGSK
LDKAAKIRAF TNYLPGFNIP MLPRELSDDL CSLRANEVRP VLACRMTLSA DGTIEDNIEF
FAATIESKAK LVYDQVSDWL ENTGDWQPES EAIAEQVRLL AQICQRRGEW RHNHALVFKD
RPDYRFILGE KGEVLDIVAE PRRIANRIVE EAMIAANICA ARVLRDKLGF GIYNVHMGFD
PANADALAAL LKTHGLHVDA EEVLTLDGFC KLRRELDAQP TGFLDSRIRR FQSFAEISTE
PGPHFGLGLE AYATWTSPIR KYGDMINHRL LKAVIKGETA TRPQDEITVQ MAERRRLNRM
AERDVGDWLY ARFLKDKAGT DTRFAAEIVD ISRGGMRVRL VDNGAIAFIP APFLHAVRDE
LVCSQENGTV QIKGETVYKV TDVIDVTIAE VRMETRSIIA RPVA
Length

644

Mol. Wt

72.492 kDa

pI

5.4 (calculated)

Extinction coefficient

65,890 - 66,765 (calc based on 11 Y, 9 W, and 7 C residues)

edit table


Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type Residues Description Notes References

Domain

189..517

PF00773 RNB domain

PMID:19920124

Domain

557..640

PF00575 S1 RNA binding domain

PMID:19920124

Domain

24..81

PF08206 Ribonuclease B OB domain

PMID:19920124

edit table

<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rnb taxon=562,83333 </beststructure>

Models

View models at:

edit table
</protect>

Structure figures

<protect>

</protect>

Notes

Gene Product Resources

[back to top]


See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type Source Notes/Reference
edit table

<protect></protect>

Notes

Accessions in Other Databases

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

NCBI (Protein) (EcoliWiki Page)

GI:16129247

Escherichia coli str. K-12 substr. MG1655

NCBI (Protein) (EcoliWiki Page)

GeneID:945864

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004320

Escherichia coli str. K-12 substr. MG1655

UniProt (EcoliWiki Page)

UniProtKB/Swiss-Prot:P30850

Escherichia coli str. K-12 substr. MG1655

EcoCyc

EcoCyc:EG11620

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG11620

Escherichia coli str. K-12 substr. MG1655

NCBI (Gene) (EcoliWiki Page)

GeneID:945864

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001568

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB1577

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]




Expression

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.


Cellular Levels

[back to top]


See Help:Cellular levels

Molecule Organism or Strain Value Units Experimental Conditions Assay used Notes Reference(s)

Protein

E. coli K-12 MC4100

7.71E+02

molecules/cell

  • Medium: median data from rich and minimal media
  • Temperature (°C): 37
  • Doubling time (min): Growth Rate(min):
  • Growth phase: other:

emPAI

PMID:18304323

Protein

E. coli K-12 MG1655

4732

molecules/cell/generation

  • Medium: MOPS Complete
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

2002

molecules/cell/generation

  • Medium: MOPS Minimal
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

Protein

E. coli K-12 MG1655

3217

molecules/cell/generation

  • Medium: MOPS Complete without Methionine
  • Temperature (°C): 37
  • Doubling time (min):
  • *Growth phase:
  • OD:
  • other:

Ribosome Profiling

PMID: 24766808

edit table

Notes

Transcription and Transcriptional Regulation

[back to top]


<protect>

See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)

rnb

edit table
Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

[back to top]


<protect><gbrowseImage> name=NC_000913:1346916..1346956 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

[back to top]


<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name Mutation Phenotype Reference
edit table


Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type Reference Notes

microarray

GEO Profiles:b1286 (EcoliWiki Page)

NCBI GEO profiles for rnb

microarray

GenExpDB:b1286 (EcoliWiki Page)

Summary of data for rnb from multiple microarray studies

edit table


Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name Resource Type Description Source Notes
edit table

<protect></protect>

Notes

Accessions Related to rnb Expression

[back to top]


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

EchoBASE

EchoBASE:EB1577

Escherichia coli str. K-12 substr. MG1655

EcoliGenExpDB (EcoliWiki Page)

EcoliGenExpDB:b1286

EcoGene

EcoGene:EG11620

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120001568

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004320

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



Evolution

[back to top]


{{#css:Suppresslinks.css}}<css>h1 .editsection { display:none;} h2 .editsection { display:none;}</css>

Homologs in Other Organisms

[back to top]


See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism Homologs (Statistics) Comments

Apis mellifera

  • ENSAPMP00000006616 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Bos taurus

  • ENSBTAP00000037928 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis briggsae

  • WBGene00034256 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Caenorhabditis elegans

  • WBGene00001001 (score: 1.000; bootstrap: 100%)

From Inparanoid:20070104

Drosophila pseudoobscura

  • GA19573-PA (score: 1.000; bootstrap: 100%)
  • GA14227-PA (score: 0.066)

From Inparanoid:20070104

Gallus gallus

  • ENSGALP00000027317 (score: 1.000; bootstrap: 100%)
  • ENSGALP00000012585 (score: 0.113)

From Inparanoid:20070104

Oryza gramene

  • Q6Z6A3 (score: 1.000; bootstrap: 100%)
  • Q9SNK4 (score: 0.110)
  • Q8H885 (score: 0.095)

From Inparanoid:20070104

Schizosaccharomyces pombe

  • SPBC26H80 (score: 1.000; bootstrap: 100%)
  • SPAC2C47c (score: 0.107)

From Inparanoid:20070104

Shigella flexneri

RNB

From SHIGELLACYC

E. coli O157

RNB

From ECOO157CYC

edit table


Do-It-Yourself Web Tools

<protect></protect>

Notes

Families

[back to top]


See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database Accession Notes

Panther (EcoliWiki Page)

PTHR23355:SF6

Pfam (EcoliWiki Page)

PF00773 RNB domain

Pfam (EcoliWiki Page)

PF00575 S1 RNA binding domain

Pfam (EcoliWiki Page)

PF08206 Ribonuclease B OB domain

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

EchoBASE

EchoBASE:EB1577

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0004320

Escherichia coli str. K-12 substr. MG1655

edit table

<protect></protect>

Notes

Links

[back to top]



References

[back to top]


See Help:References for how to manage references in EcoliWiki.

  1. ↑ 1.00 1.01 1.02 1.03 1.04 1.05 1.06 1.07 1.08 1.09 1.10 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
  2. ↑ 2.0 2.1 2.2 2.3 2.4 2.5 2.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. ↑ 3.0 3.1 3.2 3.3 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. ↑ 4.0 4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
  5. ↑ 5.0 5.1 5.2 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).

Categories

[back to top]


Retrieved from "https://ecoliwiki.org/colipedia/index.php?title=rnb:On_One_Page&oldid=219681"