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On One Page

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Expression|

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Standard Name	rraB
Gene Synonym(s)	yjgD, ECK4248, b4255, JW4212^[1]^[2], JW4212
Product Desc.	conserved hypothetical protein^[3]; ribonuclease E inhibitor protein B^[2] Protein inhibitor of RNase E, modulates global mRNA abundance when overexpressed^[4]
Product Synonyms(s)	conserved protein^[1], B4255^[3]^[1], YjgD^[3]^[1], RraB^[2]^[1] , ECK4248, JW4212, yjgD, b4255
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjgD^[3]
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	rraB
Mnemonic	Systematic nomenclature
Synonyms	yjgD, ECK4248, b4255, JW4212^[1]^[2], JW4212
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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	96.48 minutes	MG1655: 4476496..4476912 <gbrowseImage> name=NC_000913:4476496..4476912 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4461605..4462021 <gbrowseImage> name=NC_012967:4461605..4462021 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4415231..4415647 <gbrowseImage> name=NC_012759:4415231..4415647 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4483153..4483569 <gbrowseImage> name=NC_007779:4483153..4483569 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4578304..4578720 <gbrowseImage> name=NC_010473:4578304..4578720 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
ΔrraB729::kan					PMID:16738554	CGSC:106324
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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:
E1F5	Kohara Phage	Genobase	PMID:3038334
5C4	Kohara Phage	Genobase	PMID:3038334
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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:G7885	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12453	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004380	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948773	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2347	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013936	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	YjgD
Synonyms	conserved protein^[1], B4255^[3]^[1], YjgD^[3]^[1], RraB^[2]^[1] , ECK4248, JW4212, yjgD, b4255
Product description	conserved hypothetical protein^[3]; ribonuclease E inhibitor protein B^[2] Protein inhibitor of RNase E, modulates global mRNA abundance when overexpressed^[4]
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
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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	References	Evidence
Protein	aceF	PMID:15690043	Experiment(s):EBI-878990
Protein	lpdA	PMID:15690043	Experiment(s):EBI-878990
Protein	yniC	PMID:15690043	Experiment(s):EBI-878990
Protein	gshA	PMID:15690043	Experiment(s):EBI-893104
Protein	guaC	PMID:15690043	Experiment(s):EBI-893104
Protein	frlA	PMID:15690043	Experiment(s):EBI-893104
Protein	mpl	PMID:15690043	Experiment(s):EBI-893104
Protein	secA	PMID:19402753	MALDI(Z-score):18.877965
Protein	rplO	PMID:19402753	MALDI(Z-score):26.609702
Protein	guaC	PMID:19402753	LCMS(ID Probability):99.6
Protein	narG	PMID:19402753	MALDI(Z-score):18.839421
Protein	deaD	PMID:19402753	MALDI(Z-score):28.193175
Protein	rplB	PMID:19402753	MALDI(Z-score):35.203346
Protein	rluB	PMID:19402753	MALDI(Z-score):25.794222
Protein	yfiF	PMID:19402753	MALDI(Z-score):30.655322
Protein	glpC	PMID:19402753	MALDI(Z-score):39.118048
Protein	mnmG	PMID:19402753	MALDI(Z-score):27.896714
Protein	mpl	PMID:19402753	LCMS(ID Probability):99.6
Protein	gshA	PMID:19402753	LCMS(ID Probability):99.6
Protein	frlA	PMID:19402753	LCMS(ID Probability):99.6
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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 See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MANPEQLEEQ REETRLIIEE LLEDGSDPDA LYTIEHHLSA DDLETLEKAA VEAFKLGYEV TDPEELEVED GDIVICCDIL SECALNADLI DAQVEQLMTL AEKFDVEYDG WGTYFEDPNG EDGDDEDFVD EDDDGVRH
Length	138
Mol. Wt	15.602 kDa
pI	3.5 (calculated)
Extinction coefficient	11,460 - 11,835 (calc based on 4 Y, 1 W, and 3 C residues)
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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
Domain	9..113	PF06877 Protein of unknown function (DUF1260)		PMID:19920124
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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=rraB 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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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
NCBI (Protein) (EcoliWiki Page)	GI:16132077	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948773	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013936	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AF90	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G7885	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12453	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948773	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2347	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)
Protein	E. coli K-12 MC4100	6.10E+04	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	Ecoli K-12	387.707+/-2.094	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.10352+/-0.00901	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.443509615	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	10698	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	3435	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	8770	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling		PMID: 24766808
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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)
yjgD
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File:.jpg

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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_000913:4476476..4476516 source=MG1655 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
microarray	GEO Profiles:b4255 (EcoliWiki Page)	NCBI GEO profiles for rraB
microarray	GenExpDB:b4255 (EcoliWiki Page)	Summary of data for rraB from multiple microarray studies
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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 rraB Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G7885	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2347	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4255
EcoGene	EcoGene:EG12453	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004380	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013936	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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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Shigella flexneri	YJGD	From SHIGELLACYC
E. coli O157	YJGD	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:89946
Pfam (EcoliWiki Page)	PF06877 Protein of unknown function (DUF1260)
EcoCyc	EcoCyc:G7885	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12453	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120004380	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2347	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013936	Escherichia coli str. K-12 substr. MG1655
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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.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 ^1.8 ^1.9 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 ^3.6 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.

rraB:On One Page

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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 rraB Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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