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On One Page

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Gene |

Product(s) |

Expression|

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Standard Name	rpsU
Gene Synonym(s)	ECK3055, b3065, JW3037^[1], JW3037
Product Desc.	30S ribosomal subunit protein S21^[2]^[3]; Component of 30S ribosomal subunit^[2]^[3]; ribosome^[2]^[3] 30S ribosomal subunit protein S21^[4]
Product Synonyms(s)	30S ribosomal subunit protein S21^[1], B3065^[2]^[1], RpsU^[2]^[1] , ECK3055, JW3037, b3065
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rpsU^[2], rpsU-dnaG-rpoD^[2]
Regulation/Activity
Quick Links
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Notes

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rpsU has been shown to be an essential gene (Bubunenko, 2007).^[4]

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	rpsU
Mnemonic	Ribosomal protein, small
Synonyms	ECK3055, b3065, JW3037^[1], JW3037
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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	69.16 minutes	MG1655: 3208803..3209018 <gbrowseImage> name=NC_000913:3208803..3209018 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3143598..3143813 <gbrowseImage> name=NC_012967:3143598..3143813 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3095951..3096166 <gbrowseImage> name=NC_012759:3095951..3096166 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3209437..3209652 <gbrowseImage> name=NC_007779:3209437..3209652 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3306548..3306763 <gbrowseImage> name=NC_010473:3306548..3306763 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
Coding Start (SO:0000323)	MG1655	3208806	Edman degradation	PMID:765257
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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
ΔrpsU (Keio:JW3037)	deletion	deletion			PMID:16738554	Shigen
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Notes

The Keio collection^[5] lists a deletion of rpsU. The insertion in this strain is a duplication of the rpsU region.^[6]

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
JW3037	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCCCGGTAATTAAAGTACGTGA Primer 2:CCGTACAGACGAGTGCGGCGTGC
19F2	Kohara Phage	Genobase	PMID:3038334
tolC210::Tn10	Linked marker	CAG12184 = CGSC7437^[7]	est. P1 cotransduction: 30% ^[8]
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[7]	est. P1 cotransduction: 80% ^[8] Synonyms:zgh-3075::Tn10, zgj-3075::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:EG10920	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10920	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000911	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947577	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0913	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010063	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	RpsU
Synonyms	30S ribosomal subunit protein S21^[1], B3065^[2]^[1], RpsU^[2]^[1] , ECK3055, JW3037, b3065
Product description	30S ribosomal subunit protein S21^[2]^[3]; Component of 30S ribosomal subunit^[2]^[3]; ribosome^[2]^[3] 30S ribosomal subunit protein S21^[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
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001911	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018278	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00358	P	Seeded from EcoCyc (v14.0)	complete
	GO:0022627	cytosolic small ribosomal subunit	PMID:4587209	IDA: Inferred from Direct Assay		C	Data in Figure 1.	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001911	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018278	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	Subunits of 30S ribosomal subunit	could be indirect
Protein	rplO		PMID:16606699	Experiment(s):EBI-1144692
Protein	rpsE		PMID:16606699	Experiment(s):EBI-1144692
Protein	Subunits of ribosome	could be indirect
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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 MPVIKVRENE PFDVALRRFK RSCEKAGVLA EVRRREFYEK PTTERKRAKA SAVKRHAKKL ARENARRTRL Y
Length	71
Mol. Wt	8.499 kDa
pI	11.6 (calculated)
Extinction coefficient	2,980 - 3,105 (calc based on 2 Y, 0 W, and 1 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
Initiator Methionine	1	Removed	UniProt:P68679
Domain	2..58	PF01165 Ribosomal protein S21		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=rpsU 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
NCBI (Protein) (EcoliWiki Page)	GI:16130961	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947577	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010063	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P68679	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10920	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10920	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947577	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000911	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0913	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	Reference(s)
Protein	E. coli K-12 MC4100	8.85E+05	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	197851	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	39044	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	57773	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)
rpsU
rpsU-dnaG-rpoD
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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_000913:3208783..3208823 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:b3065 (EcoliWiki Page)	NCBI GEO profiles for rpsU
microarray	GenExpDB:b3065 (EcoliWiki Page)	Summary of data for rpsU 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
	GFP Fusion	Intergenic region (3208113..3208494) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:H5^[9]
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Notes

Accessions Related to rpsU Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10920	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0913	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3065
EcoGene	EcoGene:EG10920	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000911	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010063	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
Xenopus tropicalis	ENSXETP00000013941 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RPSU	From SHIGELLACYC
E. coli O157	RPSU	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
Pfam (EcoliWiki Page)	PF01165 Ribosomal protein S21
EcoCyc	EcoCyc:EG10920	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10920	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000911	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0913	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010063	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 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 ^2.11 EcoCyc (release 10.6; 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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Baba, T et al. (2006) Construction of Escherichia coli K-12 in-frame, single-gene knockout mutants: the Keio collection. Mol. Syst. Biol. 2 2006.0008 PubMed
↑ Yamamoto, N et al. (2009) Update on the Keio collection of Escherichia coli single-gene deletion mutants. Mol. Syst. Biol. 5 335 PubMed
↑ ^7.0 ^7.1 CGSC: The Coli Genetics Stock Center
↑ ^8.0 ^8.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rpsU: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 rpsU Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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