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EXOSC2 exosome component 2 [ Homo sapiens (human) ]

Gene ID: 23404, updated on 3-Nov-2024

Summary

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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
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Genomic context

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See EXOSC2 in Genome Data Viewer
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_000009.12Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133538423-133539264 Neighboring gene ribosomal protein L19 pseudogene 15 Neighboring gene VISTA enhancer hs876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:133541982-133543181 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133556829-133557504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29155 Neighboring gene PR/SET domain 12 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29157 Neighboring gene ABL breakpoint recombination region Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133587784-133588460 Neighboring gene uncharacterized LOC128092248 Neighboring gene ribosomal protein L37 pseudogene 17 Neighboring gene ABL proto-oncogene 1, non-receptor tyrosine kinase

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • 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?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
Submit: New GeneRIF Correction

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

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)

  1. 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

  2. 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

  3. 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

  1. 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

  1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    130693760..130704894
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    142898712..142909846
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    B3KQW2

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

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q13868.2 GenPept UniProtKB/Swiss-Prot:Q13868

Gene LinkOut

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