EXOSC5 exosome component 5 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EXOSC5provided by HGNC
Official Full Name: exosome component 5provided by HGNC
Primary source: HGNC:HGNC:24662
See related: Ensembl:ENSG00000077348 MIM:606492; AllianceGenome:HGNC:24662
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: p12B; CABAC; RRP46; RRP41B; Rrp46p; hRrp46p
Summary: Predicted to enable RNA binding activity. Involved in DNA deamination and exonucleolytic catabolism of deadenylated mRNA. Acts upstream of or within defense response to virus. Located in nucleolus; nucleoplasm; and transcriptionally active chromatin. Part of exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in lymph node (RPKM 8.8), ovary (RPKM 8.2) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 19q13.2

Exon count:: 6

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	19	NC_000019.10 (41386374..41397359, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	19	NC_060943.1 (44207608..44218583, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	19	NC_000019.9 (41892279..41903264, complement)

Chromosome 19 - NC_000019.10 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?

Risk of sudden cardiac death in EXOSC5-related disease.
Title: Risk of sudden cardiac death in EXOSC5-related disease.
Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness.
Title: Biallelic variants in the RNA exosome gene EXOSC5 are associated with developmental delays, short stature, cerebellar hypoplasia and motor weakness.
The roles of Prdx1 and Exosc5 in host defense mechanisms in HBV infection.
Title: Peroxiredoxin 1, a Novel HBx-Interacting Protein, Interacts with Exosome Component 5 and Negatively Regulates Hepatitis B Virus (HBV) Propagation through Degradation of HBV RNA.
Further, subcellular co-localization assay showed that the two proteins could co-localize in the cytoplasm of K562 cells, but WT1/CML28 complexes were not detected by using immunoprecipitation.
Title: Interaction of human genes WT1 and CML28 in leukemic cells.
Results suggest that Rrp46 forms a homodimer separately from exosome complexes and, depending on species, is a structural component of the machinery that cleaves DNA during apoptosis.
Title: Structural and biochemical characterization of CRN-5 and Rrp46: an exosome component participating in apoptotic DNA degradation.
rAAV/CML28-transduced DCs vaccine may serve as a feasible approach for the treatment of CML28-associated cancers.
Title: Activation of cytotoxic T lymphocytes against CML28-bearing tumors by dendritic cells transduced with a recombinant adeno-associated virus encoding the CML28 gene.
association of hCsl4p with the exosome is mediated by protein-protein interactions with hRrp42p and hRrp46p
Title: Protein-protein interactions of hCsl4p with other human exosome subunits.
These results in our study indicates gene silencing of SOCS1 remarkably enhanced the cytotoxicity efficiency of CML28 DNA vaccine in DCs.
Title: Induction of CML28-specific cytotoxic T cell responses using co-transfected dendritic cells with CML28 DNA vaccine and SOCS1 small interfering RNA expression vector.
Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring.
Title: Protein-protein interactions between human exosome components support the assembly of RNase PH-type subunits into a six-membered PNPase-like ring.

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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
Cerebellar ataxia, brain abnormalities, and cardiac conduction defects MedGen: C5562005 OMIM: 619576 GeneReviews: Not available	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 5 (EXOSC5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells	PubMed
Knockdown of exosome component 5 (EXOSC5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Knockdown of exosome component 5 (EXOSC5) affects HIV-1 Gag trafficking, leading to inhibit HIV-1 replication in Jurkat cells	PubMed
Rev	rev	HIV-1 Rev interacting protein, exosome component 5 (EXOSC5), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EXOSC5 is increased by RRE	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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Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	NAS Non-traceable Author Statement more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
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 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 U4 snRNA 3'-end processing	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within defense response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear mRNA surveillance	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 rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in rRNA processing	NAS Non-traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
located_in cytoplasm	NAS Non-traceable Author Statement more info	PubMed
part_of cytoplasmic exosome (RNase complex)	IBA Inferred from Biological aspect of Ancestor more info
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
part_of 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)	NAS Non-traceable Author Statement more info	PubMed
part_of nucleolar exosome (RNase complex)	NAS Non-traceable Author Statement more info	PubMed
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement 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 RRP46

Names: chronic myelogenous leukemia tumor antigen 28; exosome complex exonuclease RRP46; exosome component Rrp46; ribosomal RNA-processing protein 46

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_020158.4 → NP_064543.3 exosome complex component RRP46

See identical proteins and their annotated locations for NP_064543.3

Status: VALIDATED

Source sequence(s)

AC011462, AF281134

Consensus CDS

CCDS12580.1

UniProtKB/Swiss-Prot

Q32Q81, Q8NG16, Q96I89, Q9NQT4

UniProtKB/TrEMBL

B2RC50

Related

ENSP00000221233.3, ENST00000221233.9

Conserved Domains (2) summary

TIGR02065
Location:28 → 232

ECX1; archaeal exosome-like complex exonuclease 1

cd11372
Location:28 → 225

RNase_PH_RRP46; RRP46 subunit of eukaryotic exosome