rrfE:On One Page

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Gene Product(s)

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Standard Name	rrfE
Gene Synonym(s)	ECK4002, b4010, JWR0110, JWR0110
Product Desc.
Product Synonyms(s)
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression
Regulation/Activity
Quick Links
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Notes

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Gene

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Nomenclature

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Standard name	rrfE
Mnemonic	Ribosomal RNA, 5S
Synonyms	ECK4002, b4010, JWR0110, JWR0110
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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	90.76 minutes	MG1655: 4211063..4211182 <gbrowseImage> name=NC_000913:4211063..4211182 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4192713..4192832 <gbrowseImage> name=NC_012967:4192713..4192832 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4100743..4100862 <gbrowseImage> name=NC_012759:4100743..4100862 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4216630..4216749 <gbrowseImage> name=NC_007779:4216630..4216749 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4310759..4310878 <gbrowseImage> name=NC_010473:4310759..4310878 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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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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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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Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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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:
thiC39::Tn10	Linked marker	CAG18500 = CGSC7472	est. P1 cotransduction: 55% Synonyms:thi-39::Tn10
malF3089::Tn10	Linked marker	CAG12164 = CGSC7476	est. P1 cotransduction: 32%
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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
EcoCyc	EcoCyc:EG30074	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG30074	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002516	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948516	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB4237	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013109	Escherichia coli str. K-12 substr. MG1655
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Links

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Name	URL	Comments
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Product(s)

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Nomenclature

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Standard name	5S rRNA
Synonyms	5S rRNA (rrfH), 5S rRNA (rrfG), 5S rRNA (rrfF), 5S rRNA (rrfD), 5S rRNA (rrfC), 5S rRNA (rrfA), 5S rRNA (rrfB), 5S rRNA (rrfE), rrfH, rrnH
Product description	5S ribosomal RNA
EC number (for enzymes)
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Function

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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:0016072	rRNA metabolic process				P	Seeded from EcoCyc 11.1.	Missing: evidence, reference
	GO:0009281	cytosolic ribosome (sensu Bacteria)				C	Seeded from EcoCyc 11.1.	Missing: evidence, reference
	GO:0006412	translation				P	Seeded from EcoCyc 11.1.	Missing: evidence, reference
	GO:0005737	cytoplasm				C	Seeded from EcoCyc 11.1.	Missing: evidence, reference
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See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Interactions

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Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of 50S ribosomal subunit	could be indirect
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Localization

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Compartment	Description	Evidence	Reference/Source	Notes
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Structure and Physical Properties

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Physical Properties

<protect> Type rRNA Sequence UGCCUGGCGG CCGUAGCGCG GUGGUCCCAC CUGACCCCAU GCCGAACUCA GAAGUGAAAC GCCGUAGCGC CGAUGGUAGU GUGGGGUCUC CCCAUGCGAG AGUAGGGAAC UGCCAGGCAU Mol. Wt 38994.32 edit table

5S rRNA - Image courtesy of RFam

See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

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

<motif_map/>

Structure See Help:Product_structure for help entering or editing information in this section of EcoliWiki. Structures <beststructure> gene=5S_rRNA taxon=562,83333 </beststructure> Models View models at: EcoliPredict ModBase PSI-PRED Protein Quaternary Structure (PQS) Genomes TO Protein (GTOP) edit table See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

</protect> Structure figures 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 See Help:Product_resources for help with entering or editing information in this section of EcoliWiki. 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 EcoGene EcoGene: Escherichia coli str. K-12 substr. MG1655 RegulonDB RegulonDB: Escherichia coli str. K-12 substr. MG1655 EchoBASE EchoBASE: Escherichia coli str. K-12 substr. MG1655 ASAP ASAP: Escherichia coli str. K-12 substr. MG1655 edit table See Help:Product_accessions for help entering or editing information in this section of EcoliWiki. Notes Links [back to top] Name URL Comments edit table See Help:Links_table for how to enter or edit information in this section of EcoliWiki. 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) edit table Notes Transcription and Transcriptional Regulation [back to top] See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki. Transcription unit(s) rrsE-gltV-rrlE-rrfE edit table Figure courtesy of RegulonDB 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] <gbrowseImage> name=NC_000913:4211043..4211083 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus. 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] 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:b4010 (EcoliWiki Page) NCBI GEO profiles for rrfE microarray GenExpDB:b4010 (EcoliWiki Page) Summary of data for rrfE 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 GFP Fusion Intergenic region (228590..228807) fused to gfpmut2. OpenBioSystems GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:G7 edit table <protect> Notes Accessions Related to rrfE Expression [back to top] See Help:Gene_accessions for help with entering information into the Gene Accessions table. Database Accession Notes EcoCyc EcoCyc:EG30074 Escherichia coli str. K-12 substr. MG1655 EchoBASE EchoBASE:EB4237 Escherichia coli str. K-12 substr. MG1655 EcoliGenExpDB (EcoliWiki Page) EcoliGenExpDB:b4010 EcoGene EcoGene:EG30074 Escherichia coli str. K-12 substr. MG1655 RegulonDB RegulonDB:ECK120002516 Escherichia coli str. K-12 substr. MG1655 ASAP ASAP:ABE-0013109 Escherichia coli str. K-12 substr. MG1655 edit table Notes Links [back to top] Name URL Comments edit table 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 edit table See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki. Do-It-Yourself Web Tools BLAST CDD InParanoid YOGY Notes Families [back to top] See Help:Gene_accessions for help with entering information into the Gene Accessions table. Database Accession Notes EcoCyc EcoCyc: Escherichia coli str. K-12 substr. MG1655 EcoGene EcoGene: Escherichia coli str. K-12 substr. MG1655 RegulonDB RegulonDB: Escherichia coli str. K-12 substr. MG1655 EchoBASE EchoBASE: Escherichia coli str. K-12 substr. MG1655 ASAP ASAP: Escherichia coli str. K-12 substr. MG1655 edit table See Help:Evolution_families for help entering or editing information in this section of EcoliWiki. Notes Links [back to top] Name URL Comments edit table See Help:Links_table for how to enter or edit information in this section of EcoliWiki. References [back to top] See Help:References for how to manage references in EcoliWiki. Categories [back to top]