EXOSC3 exosome component 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EXOSC3provided by HGNC
Official Full Name: exosome component 3provided by HGNC
Primary source: HGNC:HGNC:17944
See related: Ensembl:ENSG00000107371 MIM:606489; AllianceGenome:HGNC:17944
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: p10; PCH1B; RRP40; Rrp40p; CGI-102; hRrp-40; bA3J10.7
Summary: This gene encodes a non-catalytic component of the human exosome, a complex with 3'-5' exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2012]
Expression: Ubiquitous expression in testis (RPKM 9.5), lymph node (RPKM 7.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9p13.2

Exon count:: 4

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (37779714..37785092, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (37803445..37808823, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (37779711..37785089, complement)

Chromosome 9 - NC_000009.12 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 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?

Potentially functional variants of INPP5D and EXOSC3 in immunity B cell-related genes are associated with non-small cell lung cancer survival.
Title: Potentially functional variants of INPP5D and EXOSC3 in immunity B cell-related genes are associated with non-small cell lung cancer survival.
Atypical hemolytic uremic syndrome induced by SARS-CoV2 infection in infants with EXOSC3 mutation.
Title: Atypical hemolytic uremic syndrome induced by SARS-CoV2 infection in infants with EXOSC3 mutation.
Aberrant expression of MYD88 via RNA-controlling CNOT4 and EXOSC3 in colonic mucosa impacts generation of colonic cancer.
Title: Aberrant expression of MYD88 via RNA-controlling CNOT4 and EXOSC3 in colonic mucosa impacts generation of colonic cancer.
Two siblings with a novel variant of EXOSC3 extended phenotypic spectrum of pontocerebellar hypoplasia 1B to an exceptionally mild form.
Title: Two siblings with a novel variant of EXOSC3 extended phenotypic spectrum of pontocerebellar hypoplasia 1B to an exceptionally mild form.
A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons.
Title: A Drosophila model of Pontocerebellar Hypoplasia reveals a critical role for the RNA exosome in neurons.
This is the first case of mitochondrial dysfunction associated with an EXOSC3 mutation, which expands the phenotypic spectrum of pontocerebellar hypoplasia type 1b.
Title: Recessive mutation in EXOSC3 associates with mitochondrial dysfunction and pontocerebellar hypoplasia.
Mutations of EXOSC3/Rrp40p associated with pontocerebellar hypoplasia with progressive cerebral atrophy impact ribosomal RNA processing functions of the exosome in S. cerevisiae.
Title: Mutations of EXOSC3/Rrp40p associated with neurological diseases impact ribosomal RNA processing functions of the exosome in S. cerevisiae.
Knock-down of rbm7, exosc8 and exosc3 in zebrafish showed a common pattern of defects in motor neurons and cerebellum. Our data indicate that impaired RNA metabolism may underlie the clinical phenotype by fine tuning gene expression which is essential for correct neuronal differentiation
Title: Altered RNA metabolism due to a homozygous RBM7 mutation in a patient with spinal motor neuropathy.
EXOSC3 mutations were linked to complicated hereditary spastic paraplegia.
Title: Novel EXOSC3 mutation causes complicated hereditary spastic paraplegia.
study identified new nonsense and missense mutations in the EXOSC3 gene and showed mutations in this gene are exclusively found in pontocerebellar hypoplasia type 1 patients; there are evident genotype-phenotype correlations in EXOSC3-mediated PCH reflected in clinical outcome, age of death and pons hypoplasia
Title: EXOSC3 mutations in pontocerebellar hypoplasia type 1: novel mutations and genotype-phenotype correlations.

Submit: New GeneRIF Correction See all GeneRIFs (14)

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

Associated conditions

Description	Tests
Pontocerebellar hypoplasia type 1B MedGen: C3553449 OMIM: 614678 GeneReviews: EXOSC3 Pontocerebellar Hypoplasia	not available

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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Replication interactions

Interaction	Pubs
Knockdown of exosome component 3 (EXOSC3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl 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

D11S2921 (e-PCR)
- UniSTS:152074

RH71167 (e-PCR)
- UniSTS:92568

D19S1122 (e-PCR)
- UniSTS:83109

Potential readthrough

Included genes: SHB, SLC25A51, TOMM5

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	NAS Non-traceable Author Statement more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
NOT enables RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in CUT catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in CUT catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA deamination	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA catabolic process	IDA Inferred from Direct Assay more info	PubMed
involved_in RNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in TRAMP-dependent tRNA surveillance pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in U4 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)	IBA Inferred from Biological aspect of Ancestor more info
involved_in isotype switching	ISS Inferred from Sequence or Structural Similarity more info
involved_in mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in poly(A)-dependent snoRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of isotype switching	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	IDA Inferred from Direct Assay more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
part_of cytoplasmic exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of cytoplasmic exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
part_of cytoplasmic exosome (RNase complex)	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 euchromatin	IMP Inferred from Mutant Phenotype more info	PubMed
part_of exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
part_of exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
part_of nuclear exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
part_of nuclear exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
part_of nuclear exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
part_of nucleolar exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: exosome complex component RRP40

Names: exosome complex exonuclease RRP40; ribosomal RNA-processing protein 40

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.

Genomic

NG_032780.1 RefSeqGene

Range

5029..10379

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001002269.2 → NP_001002269.1 exosome complex component RRP40 isoform 2

See identical proteins and their annotated locations for NP_001002269.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an exon in the coding region that causes a frameshift and leads to an early stop codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.

Source sequence(s)

AF229833, AK290864, BE048144, BP237222, DA352003

Consensus CDS

CCDS43805.1

UniProtKB/Swiss-Prot

Q9NQT5

UniProtKB/TrEMBL

Q9NYS3

Related

ENSP00000379775.3, ENST00000396521.3

Conserved Domains (1) summary

cl09927
Location:108 → 159

S1_like; S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. ...
NM_016042.4 → NP_057126.2 exosome complex component RRP40 isoform 1

See identical proteins and their annotated locations for NP_057126.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AF281132, AK290864, BE048144

Consensus CDS

CCDS35016.1

UniProtKB/Swiss-Prot

A8K0K6, Q5QP85, Q9NQT5, Q9Y3A8

Related

ENSP00000323046.4, ENST00000327304.10

Conserved Domains (2) summary

cd05790
Location:108 → 193

S1_Rrp40; S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation ...

cl26026
Location:26 → 274

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region