ryeB:On One Page

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

Quickview

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Standard Name

ryeB

Gene Synonym(s)

ECK1839, b4433, JWR0238, tpke79, tkpe79[1][2]

Product Desc.

small RNA that interacts with Hfq[2][3]

Product Synonyms(s)

small RNA[1], RyeB[2][1], Tkpe79[2][1]

Function from GO

<GO_nr />

Knock-Out Phenotype
Regulation/Expression

transcription unit(s): ryeB[2]

Regulation/Activity
Quick Links

porteco.png EcoCyc.gif regulondb.jpg

dnadisplay.png pubmed.jpg   textpresso.jpg  

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Notes

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Gene

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Nomenclature

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

Standard name

ryeB

Mnemonic

Systematic nomenclature

Synonyms

ECK1839, b4433, JWR0238, tpke79, tkpe79[1][2]

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Notes

Location(s) and DNA Sequence

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<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

41.41 minutes, 41.41 minutes 

MG1655: 1921308..1921188
<gbrowseImage> name=NC_000913:1921188..1921308 source=MG1655 preset=GeneLocation </gbrowseImage>

BW2952

NC_012759: 1813247..1813367
<gbrowseImage> name=NC_012759:1813247..1813367 source=BW2952 preset=GeneLocation </gbrowseImage>

W3110

 

W3110: 1924998..1924878
<gbrowseImage> name=NC_007779:1924878..1924998 source=W3110 preset=GeneLocation </gbrowseImage>

DH10B

DH10B: 2011879..2011759
<gbrowseImage> name=NC_010473:2011759..2011879 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

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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

Plasmid clone

Shigen

PMID:16769691

Status:

Primer 1:

Primer 2:

19H3

Kohara Phage

Genobase

PMID:3038334

zea-225::Tn10

Linked marker

CAG18465 = CGSC7388[4]

est. P1 cotransduction: 9% [5]
Synonyms:zdj-225::Tn10

eda-51::Tn10

Linked marker

CAG18486 = CGSC7392[4]

est. P1 cotransduction: 74% [5]

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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:G0-8883

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG31147

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002594

Escherichia coli str. K-12 substr. MG1655

NCBI (EcoliWiki Page)

GeneID:2847772

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4515

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0047253

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Product(s)

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Nomenclature

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

Standard name

RyeB RNA

Synonyms

small RNA[1], RyeB[2][1], Tkpe79[2][1]

Product description

small RNA that interacts with Hfq[2][3]

EC number (for enzymes)


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Notes

Function

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<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

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

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Notes

Localization

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

Compartment Description Evidence Reference/Source Notes

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Notes

Structure and Physical Properties

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<protect> Physical Properties

Type

sRNA

Sequence
GCUGAUGACC ACCACGCUUU UUAUUGACCA UUUUGCACGC AAACUGGAAA ACCUGGCGUC
GUCAUCUAUU CUUAAAGGGC AAGGCAACUA AGCCUGCAUU AAUGCCAACU UUUAGCGCAC G
Mol. Wt

38871.17


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

<motif_map/>

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

Structures

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

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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

Resource type Source Notes/Reference

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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:G0-8883

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG31147

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002594

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4515

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0047253

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Expression

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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

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See Help:Cellular levels

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

Notes

Transcription and Transcriptional Regulation

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

Transcription unit(s)

ryeB

Figure courtesy of RegulonDB

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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

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<protect><gbrowseImage> name=NC_000913:1921288..1921328 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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

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

Allele Name Mutation Phenotype Reference


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

Type Reference Notes


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

Resource Name Resource Type Description Source Notes

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Notes

Accessions Related to ryeB Expression

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

Database Accession Notes

EcoCyc

EcoCyc:G0-8883

Escherichia coli str. K-12 substr. MG1655

EchoBASE

EchoBASE:EB4515

Escherichia coli str. K-12 substr. MG1655

EcoGene

EcoGene:EG31147

Escherichia coli str. K-12 substr. MG1655

RegulonDB

RegulonDB:ECK120002594

Escherichia coli str. K-12 substr. MG1655

ASAP

ASAP:ABE-0047253

Escherichia coli str. K-12 substr. MG1655

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Notes

Links

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Evolution

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Homologs in Other Organisms

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

Organism Homologs (Statistics) Comments

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Do-It-Yourself Web Tools

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Notes

Families

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Database Accession Notes

PFAM (EcoliWiki Page)

PFAM:PF00149

edit table

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Notes

Families

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<protect> See Help:Evolution_families for help entering or editing information in this section of EcoliWiki.

Database Accession Notes

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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. 1.0 1.1 1.2 1.3 1.4 1.5 1.6 1.7 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 2.7 2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  3. 3.0 3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
  4. 4.0 4.1 CGSC: The Coli Genetics Stock Center
  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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