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Expression|

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Standard Name	ryhB
Gene Synonym(s)	ECK3426, b4451, JWR0219, fer, sraI, IS176, psrA18^[1], psrA18
Product Desc.	regulatory antisense RNA involved in iron homeostasis^[2]^[3]
Product Synonyms(s)	regulatory sRNA^[1], SraI^[2]^[1], PsrA18^[2]^[1], RyhB^[2]^[1], IS176^[2]^[1]
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ryhB^[2]
Regulation/Activity
Quick Links
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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	ryhB
Mnemonic	Systematic nomenclature
Synonyms	ECK3426, b4451, JWR0219, fer, sraI, IS176, psrA18^[1], psrA18
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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	77.14 minutes	MG1655: 3579039..3578946 <gbrowseImage> name=NC_000913:3578946..3579039 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3467444..3467533 <gbrowseImage> name=NC_012759:3467444..3467533 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4059399..4059492 <gbrowseImage> name=NC_007779:4059399..4059492 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3676784..3676691 <gbrowseImage> name=NC_010473:3676691..3676784 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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
Over production of RyhB			Growth Phenotype	Unable to grow on succinate minimal plates	PMID:11917098
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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:
10F5	Kohara Phage	Genobase	PMID:3038334
16A5	Kohara Phage	Genobase	PMID:3038334
glgP721::Tn10	Linked marker	CAG18638 = CGSC7451^[4]	est. P1 cotransduction: 57% ^[5] Synonyms:zhg-3086::Tn10, zhh-21::Tn10
zhg-50::Tn10	Linked marker	CAG18450 = CGSC7450^[4]	est. P1 cotransduction: 66% ^[5] Synonyms:zhf-50::Tn10, zhf-5::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:G0-8872	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG31133	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002584	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:2847761	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4294	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0047271	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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	RyhB RNA
Synonyms	regulatory sRNA^[1], SraI^[2]^[1], PsrA18^[2]^[1], RyhB^[2]^[1], IS176^[2]^[1]
Product description	regulatory antisense RNA involved in iron homeostasis^[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	Aspect	Notes	Status
	GO:0040033	negative regulation of translation, ncRNA-mediated	PMID:14617150	IDA: Inferred from Direct Assay	P	Seeded from EcoCyc (v14.0)	complete
	GO:0040033	negative regulation of translation, ncRNA-mediated	PMID:17264113	IEP: Inferred from Expression Pattern	P		complete
	GO:0070928	regulation of mRNA stability, ncRNA-mediated	PMID:12975324	IDA: Inferred from Direct Assay	P	Seeded from EcoCyc (v14.0)	complete
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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	Fur	represses ryhB synthesis in the presence of iron	PMID:11917098	fur- mutant derepresses RyhB synthesis
Protein	Hfq RNA binding protein	RyhB depends on Hfq RNA-binding protein for function	PMID:11917098	hfq mutant reverses the effect of fur- mutatns for growth on succinate and fumarate; hfq mutant acts phenotypically like an ryhB- strain
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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	GCGAUCAGGA AGACCCUCGC GGAGAACCUG AAAGCACGAC AUUGCUCACA UUGCUUCCAG UAUUACUUAG CCAGCCGGGU GCUGGCUUUU
Mol. Wt	29071.31
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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
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<motif_map/>

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

Structures

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

Models

View models at:

PSI-PRED
Genomes TO Protein (GTOP)

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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:G0-8872	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG31133	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002584	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4294	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0047271	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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)
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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)
ryhB
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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_000913:3579019..3579059 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
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
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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 ryhB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G0-8872	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4294	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG31133	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002584	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0047271	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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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

Notes

Families

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Database	Accession	Notes
PFAM (EcoliWiki Page)	PFAM:PF01408
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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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Name	URL	Comments
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References

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

↑ ^1.00 ^1.01 ^1.02 ^1.03 ^1.04 ^1.05 ^1.06 ^1.07 ^1.08 ^1.09 ^1.10 ^1.11 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 CGSC: The Coli Genetics Stock Center
↑ ^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).

ryhB:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to ryhB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Families

Notes

Links

References

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