EXOSC10 exosome component 10 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EXOSC10provided by HGNC
Official Full Name: exosome component 10provided by HGNC
Primary source: HGNC:HGNC:9138
See related: Ensembl:ENSG00000171824 MIM:605960; AllianceGenome:HGNC:9138
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: p2; p3; p4; RRP6; PMSCL; Rrp6p; PM-Scl; PMSCL2; PM/Scl-100
Summary: Enables 3'-5'-exoribonuclease activity. Involved in several processes, including RNA catabolic process; maturation of 5.8S rRNA; and negative regulation of telomere maintenance via telomerase. Located in cytosol; nuclear lumen; and transcriptionally active chromatin. Part of nuclear exosome (RNase complex). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Ubiquitous expression in skin (RPKM 18.4), testis (RPKM 18.0) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p36.22

Exon count:: 26

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (11066618..11099869, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (10608183..10641440, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (11126675..11159926, complement)

Chromosome 1 - NC_000001.11 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?

Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile.
Title: Hypoxia-driven deSUMOylation of EXOSC10 promotes adaptive changes in the transcriptome profile.
EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification.
Title: EXOSC10 is a novel hepatocellular carcinoma prognostic biomarker: a comprehensive bioinformatics analysis and experiment verification.
The ubiquitin-specific protease USP36 SUMOylates EXOSC10 and promotes the nucleolar RNA exosome function in rRNA processing.
Title: The ubiquitin-specific protease USP36 SUMOylates EXOSC10 and promotes the nucleolar RNA exosome function in rRNA processing.
MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.
Title: MPP6 stimulates both RRP6 and DIS3 to degrade a specified subset of MTR4-sensitive substrates in the human nucleus.
The clinical phenotype of systemic sclerosis patients with anti-PM/Scl antibodies: results from the EUSTAR cohort.
Title: The clinical phenotype of systemic sclerosis patients with anti-PM/Scl antibodies: results from the EUSTAR cohort.
RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis.
Title: RNA-regulatory exosome complex confers cellular survival to promote erythropoiesis.
Exploration of Salmonella effector mutant strains on MTR4 and RRP6 degradation.
Title: Exploration of Salmonella effector mutant strains on MTR4 and RRP6 degradation.
Authors engineered cells in which the 3'-->5' exoribonucleases of the exosome complex, DIS3 and EXOSC10, can be rapidly eliminated to assess their immediate roles in nuclear RNA biology. These transcripts are unaffected by the rapid loss of EXOSC10, suggesting that they are rarely targeted to it.
Title: Rapid Depletion of DIS3, EXOSC10, or XRN2 Reveals the Immediate Impact of Exoribonucleolysis on Nuclear RNA Metabolism and Transcriptional Control.
Study shows that the catalytic activity of the exosome subunit EXOSC10 contributes to the homologous recombination (HR) pathway by degrading damage-induced lncRNAs and maintaining RNA homeostasis at double-strand breaks (DSBs). Results identify RNA clearance at DSBs as a step in the HR pathway that is required for the assembly of RPA onto the resected ssDNA, which in turn is a prerequisite for controlled DNA resection.
Title: EXOSC10 is required for RPA assembly and controlled DNA end resection at DNA double-strand breaks.
Processing of 3' telomerase RNA occurs in two steps with longer forms first being trimmed by RRP6 and shorter forms then being processed by PARN.
Title: The H/ACA complex disrupts triplex in hTR precursor to permit processing by RRP6 and PARN.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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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Replication interactions

Interaction	Pubs
Knockdown of exosome component 10 (EXOSC10) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Interaction of HIV-1 Gag with exosome component 10 (EXOSC10) is identified in a series of six affinity purification/mass spectrometry screens	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

RH78022 (e-PCR)
- UniSTS:66059

RH44136 (e-PCR)
- UniSTS:58902

D1S1383 (e-PCR)
- UniSTS:149579

SHGC-32065 (e-PCR)
- UniSTS:12429

RH71349 (e-PCR)
- UniSTS:41373

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3'-5'-RNA exonuclease activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables 3'-5'-RNA exonuclease activity	TAS Traceable Author Statement more info
enables RNA binding	HDA more info	PubMed
enables RNA exonuclease activity	IDA Inferred from Direct Assay more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleotide binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables single-stranded RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables telomerase RNA binding	IC Inferred by Curator more info	PubMed

Process	Evidence Code	Pubs
involved_in CUT catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA repair	IEA Inferred from Electronic Annotation more info
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 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 histone mRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in histone mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in maturation of 5.8S rRNA	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of telomere maintenance via telomerase	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear mRNA surveillance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent CUT catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear polyadenylation-dependent antisense transcript catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear polyadenylation-dependent rRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear polyadenylation-dependent snRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear polyadenylation-dependent snoRNA catabolic process	IBA Inferred from Biological aspect of Ancestor more info
involved_in nuclear-transcribed mRNA catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation 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 mRNA cis splicing, via spliceosome	IEA Inferred from Electronic Annotation more info
involved_in rRNA processing	TAS Traceable Author Statement more info
involved_in regulation of telomerase RNA localization to Cajal body	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in ribosomal small subunit biogenesis	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)	NAS Non-traceable Author Statement more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
part_of euchromatin	IMP Inferred from Mutant Phenotype more info	PubMed
part_of exosome (RNase complex)	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	HDA 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
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 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
part_of small-subunit processome	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: exosome complex component 10; exosome component 10

Names: P100 polymyositis-scleroderma overlap syndrome-associated autoantigen; autoantigen PM-SCL; polymyositis/scleroderma autoantigen 100 kDa; polymyositis/scleroderma autoantigen 2

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_001001998.3 → NP_001001998.1 exosome complex component 10 isoform 1

See identical proteins and their annotated locations for NP_001001998.1

Status: VALIDATED

Description

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

Source sequence(s)

BC028687, BC073788, CA307576

Consensus CDS

CCDS30584.1

UniProtKB/Swiss-Prot

B1AKQ0, B1AKQ1, Q01780, Q15158

Related

ENSP00000366135.4, ENST00000376936.9

Conserved Domains (3) summary

cd06147
Location:284 → 474

Rrp6p_like_exo; DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins

smart00341
Location:503 → 583

HRDC; Helicase and RNase D C-terminal

pfam08066
Location:47 → 133

PMC2NT; PMC2NT (NUC016) domain
NM_002685.4 → NP_002676.1 exosome complex component 10 isoform 2

See identical proteins and their annotated locations for NP_002676.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

BC028687, BC073788, CA307576, L01457

Consensus CDS

CCDS126.1

UniProtKB/Swiss-Prot

Q01780

Related

ENSP00000307307.7, ENST00000304457.11

Conserved Domains (3) summary

cd06147
Location:284 → 474

Rrp6p_like_exo; DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins

smart00341
Location:503 → 583

HRDC; Helicase and RNase D C-terminal

pfam08066
Location:46 → 132

PMC2NT; PMC2NT (NUC016) domain

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

11066618..11099869 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005263475.3 → XP_005263532.2 exosome component 10 isoform X1

Conserved Domains (3) summary

cd06147
Location:284 → 474

Rrp6p_like_exo; DEDDy 3'-5' exonuclease domain of yeast Rrp6p, human polymyositis/scleroderma autoantigen 100kDa, and similar proteins

smart00341
Location:503 → 583

HRDC; Helicase and RNase D C-terminal

pfam08066
Location:46 → 132

PMC2NT; PMC2NT (NUC016) domain
XM_047422661.1 → XP_047278617.1 exosome component 10 isoform X2
XM_047422663.1 → XP_047278619.1 exosome component 10 isoform X3