RPS3 ribosomal protein S3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: RPS3provided by HGNC
Official Full Name: ribosomal protein S3provided by HGNC
Primary source: HGNC:HGNC:10420
See related: Ensembl:ENSG00000149273 MIM:600454; AllianceGenome:HGNC:10420
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: S3; uS3
Summary: Ribosomes, the organelles that catalyze protein synthesis, consist of a small 40S subunit and a large 60S subunit. Together these subunits are composed of 4 RNA species and approximately 80 structurally distinct proteins. This gene encodes a ribosomal protein that is a component of the 40S subunit, where it forms part of the domain where translation is initiated. The protein belongs to the S3P family of ribosomal proteins. Studies of the mouse and rat proteins have demonstrated that the protein has an extraribosomal role as an endonuclease involved in the repair of UV-induced DNA damage. The protein appears to be located in both the cytoplasm and nucleus but not in the nucleolus. Higher levels of expression of this gene in colon adenocarcinomas and adenomatous polyps compared to adjacent normal colonic mucosa have been observed. This gene is co-transcribed with the small nucleolar RNA genes U15A and U15B, which are located in its first and fifth introns, respectively. As is typical for genes encoding ribosomal proteins, there are multiple processed pseudogenes of this gene dispersed through the genome. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, May 2012]
Expression: Ubiquitous expression in ovary (RPKM 566.1), bone marrow (RPKM 278.4) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.4

Exon count:: 8

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (75399518..75422302)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (75329106..75351811)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (75110562..75133346)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phosphorylation of rpS3 by Lyn increases translation of Multi-Drug Resistance (MDR1) gene.
Title: Phosphorylation of rpS3 by Lyn increases translation of Multi-Drug Resistance (MDR1) gene.
Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding.
Title: Selective translational control of cellular and viral mRNAs by RPS3 mRNA binding.
UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3.
Title: UBE2J1 inhibits colorectal cancer progression by promoting ubiquitination and degradation of RPS3.
AP lyase activity of the human ribosomal protein uS3: The DNA cleavage sequence specificity and the location of the enzyme active center.
Title: AP lyase activity of the human ribosomal protein uS3: The DNA cleavage sequence specificity and the location of the enzyme active center.
RPS3 predicts poor overall survival in HBV-related hepatocellular carcinoma patients: a data-mining with LASSO-regression algorithm.
Title: RPS3 predicts poor overall survival in HBV-related hepatocellular carcinoma patients: a data-mining with LASSO-regression algorithm.
Mesothelinspecific T cell cytotoxicity against triple negative breast cancer is enhanced by 40s ribosomal protein subunit 3treated selfdifferentiated dendritic cells.
Title: Mesothelin‑specific T cell cytotoxicity against triple negative breast cancer is enhanced by 40s ribosomal protein subunit 3‑treated self‑differentiated dendritic cells.
A novel NF-kappaB regulator encoded by circPLCE1 inhibits colorectal carcinoma progression by promoting RPS3 ubiquitin-dependent degradation.
Title: A novel NF-κB regulator encoded by circPLCE1 inhibits colorectal carcinoma progression by promoting RPS3 ubiquitin-dependent degradation.
Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3.
Title: Fucosylated Proteome Profiling Identifies a Fucosylated, Non-Ribosomal, Stress-Responsive Species of Ribosomal Protein S3.
Ribosomal protein S3 selectively affects colon cancer growth by modulating the levels of p53 and lactate dehydrogenase.
Title: Ribosomal protein S3 selectively affects colon cancer growth by modulating the levels of p53 and lactate dehydrogenase.
Ribosomal protein S3-derived repair domain peptides regulate UV-induced matrix metalloproteinase-1.
Title: Ribosomal protein S3-derived repair domain peptides regulate UV-induced matrix metalloproteinase-1.

Submit: New GeneRIF Correction See all GeneRIFs (49)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify ribosomal protein S3 (RPS3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify ribosomal protein S3 (RPS3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify ribosomal protein S3 (RPS3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	HIV-1 Gag interacts with RPS3 as demonstrated by proximity dependent biotinylation proteomics	PubMed
	gag	Tandem affinity purification and mass spectrometry analysis identify ribosomal protein S3 (RPS3), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D11S1962 (e-PCR)
- UniSTS:28490

RH35764 (e-PCR)
- UniSTS:59756

MARC_4995-4996:996679647:1 (e-PCR)
- UniSTS:269430

A005D09 (e-PCR)
- UniSTS:68034

RH68863 (e-PCR)
- UniSTS:91855

RH94000 (e-PCR)
- UniSTS:92157

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
NOT enables DNA N-glycosylase activity	IDA Inferred from Direct Assay more info	PubMed
NOT enables DNA N-glycosylase activity	TAS Traceable Author Statement more info	PubMed
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-(apurinic or apyrimidinic site) endonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables Hsp70 protein binding	IDA Inferred from Direct Assay more info	PubMed
enables Hsp90 protein binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IDA Inferred from Direct Assay more info	PubMed
contributes_to RNA polymerase II transcription regulatory region sequence-specific DNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables class I DNA-(apurinic or apyrimidinic site) endonuclease activity	IEA Inferred from Electronic Annotation more info
enables damaged DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables enzyme binding	IPI Inferred from Physical Interaction more info	PubMed
enables iron-sulfur cluster binding	NAS Non-traceable Author Statement more info	PubMed
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables microtubule binding	IDA Inferred from Direct Assay more info	PubMed
enables oxidized purine DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables oxidized pyrimidine DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase A binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables small ribosomal subunit rRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables structural constituent of ribosome	HDA more info	PubMed
enables structural constituent of ribosome	IBA Inferred from Biological aspect of Ancestor more info
enables structural constituent of ribosome	IDA Inferred from Direct Assay more info	PubMed
enables structural constituent of ribosome	NAS Non-traceable Author Statement more info	PubMed
enables supercoiled DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables tubulin binding	IDA Inferred from Direct Assay more info	PubMed
enables ubiquitin-like protein conjugating enzyme binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in DNA damage response	IEP Inferred from Expression Pattern more info	PubMed
involved_in DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in apoptotic process	IEA Inferred from Electronic Annotation more info
involved_in base-excision repair	IDA Inferred from Direct Assay more info	PubMed
involved_in cell division	IEA Inferred from Electronic Annotation more info
involved_in cellular response to hydrogen peroxide	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to reactive oxygen species	IDA Inferred from Direct Assay more info	PubMed
involved_in cellular response to tumor necrosis factor	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chromosome segregation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cytoplasmic translation	IC Inferred by Curator more info	PubMed
involved_in cytoplasmic translation	NAS Non-traceable Author Statement more info	PubMed
involved_in negative regulation of DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of DNA repair	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of JUN kinase activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	IGI Inferred from Genetic Interaction more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of T cell receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of activated T cell proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of apoptotic signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of apoptotic signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of base-excision repair	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of endodeoxyribonuclease activity	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of gene expression	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-2 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of intrinsic apoptotic signaling pathway in response to DNA damage	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of microtubule polymerization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of non-canonical NF-kappaB signal transduction	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein-containing complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of apoptotic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to TNF agonist	IDA Inferred from Direct Assay more info	PubMed
involved_in spindle assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in translation	IC Inferred by Curator more info	PubMed
involved_in translation	NAS Non-traceable Author Statement more info	PubMed
involved_in translational initiation	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of NF-kappaB complex	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IMP Inferred from Mutant Phenotype more info	PubMed
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
located_in cytosolic ribosome	IDA Inferred from Direct Assay more info	PubMed
part_of cytosolic small ribosomal subunit	HDA more info	PubMed
part_of cytosolic small ribosomal subunit	IBA Inferred from Biological aspect of Ancestor more info
part_of cytosolic small ribosomal subunit	IDA Inferred from Direct Assay more info	PubMed
part_of cytosolic small ribosomal subunit	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in extracellular exosome	HDA more info	PubMed
located_in focal adhesion	HDA more info	PubMed
located_in membrane	HDA more info	PubMed
located_in mitochondrial inner membrane	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrial matrix	IDA Inferred from Direct Assay more info	PubMed
located_in mitotic spindle	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleus	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in postsynaptic density	EXP Inferred from Experiment more info	PubMed
is_active_in postsynaptic density	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
located_in ribosome	IDA Inferred from Direct Assay more info	PubMed
located_in ruffle membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: small ribosomal subunit protein uS3

Names: 40S ribosomal protein S3; IMR-90 ribosomal protein S3

NP_000996.2

EC 4.2.99.18

NP_001243731.1

EC 4.2.99.18

NP_001247435.1

EC 4.2.99.18

NP_001247436.1

EC 4.2.99.18

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_001005.5 → NP_000996.2 small ribosomal subunit protein uS3 isoform 1

See identical proteins and their annotated locations for NP_000996.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) and variant 2 both encode the same protein (isoform 1).

Source sequence(s)

AP000744, BC034149, CB241053

Consensus CDS

CCDS8236.1

UniProtKB/Swiss-Prot

B2R7N5, J3KN86, P23396, Q498B5, Q8NI95

UniProtKB/TrEMBL

E9PL09

Related

ENSP00000434643.1, ENST00000531188.6

Conserved Domains (1) summary

PTZ00084
Location:4 → 216

PTZ00084; 40S ribosomal protein S3; Provisional
NM_001256802.2 → NP_001243731.1 small ribosomal subunit protein uS3 isoform 1

See identical proteins and their annotated locations for NP_001243731.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 3' UTR compared to variant 1. Variants 1 and 2 both encode the same protein (isoform 1).

Source sequence(s)

AA976344, AW134501, BC034149

Consensus CDS

CCDS8236.1

UniProtKB/Swiss-Prot

B2R7N5, J3KN86, P23396, Q498B5, Q8NI95

UniProtKB/TrEMBL

E9PL09

Related

ENSP00000436971.1, ENST00000527446.5

Conserved Domains (1) summary

PTZ00084
Location:4 → 216

PTZ00084; 40S ribosomal protein S3; Provisional
NM_001260506.2 → NP_001247435.1 small ribosomal subunit protein uS3 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (3) has two additional segments, one in the coding region and one in the 3' UTR, compared to variant 1. The resulting isoform (2) is longer and has an additional segment in the central region, compared to isoform 1.

Source sequence(s)

AP000744, BM831460, BM928330, BQ645330, CB241053, DW448503

Consensus CDS

CCDS58161.1

UniProtKB/TrEMBL

E9PL09

Related

ENSP00000278572.6, ENST00000278572.10

Conserved Domains (1) summary

PTZ00084
Location:4 → 232

PTZ00084; 40S ribosomal protein S3; Provisional
NM_001260507.2 → NP_001247436.1 small ribosomal subunit protein uS3 isoform 3

See identical proteins and their annotated locations for NP_001247436.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks an exon in the 5' region, which results in a downstream start codon, compared to variant 1. The resulting isoform (3) has a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AP000744, BC013231, BE797417, BM831460, CB241053

UniProtKB/TrEMBL

E9PSF4

Related

ENSP00000416745.2, ENST00000422465.6

Conserved Domains (1) summary

PTZ00084
Location:1 → 90

PTZ00084; 40S ribosomal protein S3; Provisional