EXOSC2 exosome component 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: EXOSC2provided by HGNC
Official Full Name: exosome component 2provided by HGNC
Primary source: HGNC:HGNC:17097
See related: Ensembl:ENSG00000130713 MIM:602238; AllianceGenome:HGNC:17097
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: p7; RRP4; SHRF; Rrp4p; hRrp4p
Summary: Predicted to enable RNA binding activity. Involved in RNA catabolic process; RNA processing; and positive regulation of cell growth. Located in cytoplasm; nucleolus; and nucleoplasm. Part of cytosol and nuclear exosome (RNase complex). Implicated in short stature, hearing loss, retinitis pigmentosa, and distinctive facies. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in lymph node (RPKM 5.3), ovary (RPKM 5.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q34.12

Exon count:: 9

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (130693760..130704894)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (142898712..142909846)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (133569147..133580281)

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?

Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
Title: Low expression of EXOSC2 protects against clinical COVID-19 and impedes SARS-CoV-2 replication.
A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex.
Title: A budding yeast model for human disease mutations in the EXOSC2 cap subunit of the RNA exosome complex.
Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis.
Title: Genetic and genomic studies of pathogenic EXOSC2 mutations in the newly described disease SHRF implicate the autophagy pathway in disease pathogenesis.
The EXOSC2-associated phenotype shows only minimal overlap with the previously reported diseases associated with mutations.
Title: Mutations in EXOSC2 are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt.
Knock-down of hRrp41p or hRrp4p but not PM/Scl-100 or PM/Scl-75 leads to codepletion of other subunits.
Title: Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways.
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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Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndrome MedGen: C4540367 OMIM: 617763 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 2 (EXOSC2; RRP4) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-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

D10S275 (e-PCR)
- UniSTS:147992

L17705 (e-PCR)
- UniSTS:66091

D8S2279 (e-PCR)
- UniSTS:473907

L18426 (e-PCR)
- UniSTS:34648

D11S3430 (e-PCR)
- UniSTS:152671

D15S1477 (e-PCR)
- UniSTS:474482

WI-11508 (e-PCR)
- UniSTS:73435

RH26892 (e-PCR)
- UniSTS:90344

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5'-RNA exonuclease activity	TAS Traceable Author Statement more info	PubMed
enables 7S RNA binding	TAS 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 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 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 cell growth	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rRNA processing	TAS Traceable Author Statement 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)	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 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 RRP4

Names: exosome complex exonuclease RRP4; homolog of yeast RRP4 (ribosomal RNA processing 4), 3' 5' exoribonuclease (RRP4); homolog of yeast RRP4 (ribosomal RNA processing 4), 3'-5'-exoribonuclease; ribosomal RNA-processing protein 4

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_001282708.1 → NP_001269637.1 exosome complex component RRP4 isoform 2

See identical proteins and their annotated locations for NP_001269637.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an alternate in-frame exon in the central coding region compared to variant 1. It encodes isoform 2 which is shorter than isoform 1.

Source sequence(s)

AK296605, AL359092, BU934039

Consensus CDS

CCDS65160.1

UniProtKB/TrEMBL

A0A8I5KVY3

Related

ENSP00000444917.1, ENST00000546165.6

Conserved Domains (1) summary

cl26026
Location:22 → 215

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
NM_001282709.1 → NP_001269638.1 exosome complex component RRP4 isoform 3

See identical proteins and their annotated locations for NP_001269638.1

Status: VALIDATED

Description

Transcript Variant: This variant (3) lacks an alternate in-frame exon in the central coding region compared to variant 1. It encodes isoform 3 which is shorter than isoform 1.

Source sequence(s)

AL359092, AL573310, BU934039, DA813307

Consensus CDS

CCDS65161.1

UniProtKB/TrEMBL

A3KFL2

Related

ENSP00000361426.3, ENST00000372351.7

Conserved Domains (1) summary

cl26026
Location:22 → 211

ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
NM_014285.7 → NP_055100.2 exosome complex component RRP4 isoform 1

See identical proteins and their annotated locations for NP_055100.2

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes the longest isoform (1).

Source sequence(s)

AL359092, BC000747, BU934039

Consensus CDS

CCDS6935.1

UniProtKB/Swiss-Prot

A3KFL3, A3KFL4, B4DKK6, Q13868, Q9NUY4

UniProtKB/TrEMBL

A3KFL2

Related

ENSP00000361433.5, ENST00000372358.10

Conserved Domains (1) summary

COG1097
Location:22 → 241

Rrp4; Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Translation, ribosomal structure and biogenesis]

RNA

NR_104230.1 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (4) lacks an alternate internal exon and uses an alternate splice site, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AK303163, AL359092

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

130693760..130704894

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005272176.3 → XP_005272233.1 exosome complex component RRP4 isoform X1

See identical proteins and their annotated locations for XP_005272233.1

UniProtKB/TrEMBL

B3KQW2

Related

ENST00000430138.7

Conserved Domains (2) summary

cd05789
Location:2 → 54

S1_Rrp4; S1_Rrp4: Rrp4 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 in ...

pfam15985
Location:57 → 97

KH_6; KH domain
XM_006717023.3 → XP_006717086.1 exosome complex component RRP4 isoform X2

Conserved Domains (2) summary

pfam15985
Location:39 → 79

KH_6; KH domain

cl09927
Location:1 → 36

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. ...

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

142898712..142909846

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054362548.1 → XP_054218523.1 exosome complex component RRP4 isoform X1

UniProtKB/TrEMBL

B3KQW2
XM_054362549.1 → XP_054218524.1 exosome complex component RRP4 isoform X2