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EXOSC9 exosome component 9 [ Homo sapiens (human) ]

Gene ID: 5393, updated on 11-Apr-2024

Summary

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Official Symbol
EXOSC9provided by HGNC
Official Full Name
exosome component 9provided by HGNC
Primary source
HGNC:HGNC:9137
See related
Ensembl:ENSG00000123737 MIM:606180; AllianceGenome:HGNC:9137
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
p5; p6; PCH1D; RRP45; PMSCL1; Rrp45p; PM/Scl-75
Summary
This gene encodes a component of the human exosome, a exoribonuclease complex which processes and degrades RNA in the nucleus and cytoplasm. This component may play a role in mRNA degradation and the polymyositis/scleroderma autoantigen complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Expression
Broad expression in testis (RPKM 24.9), bone marrow (RPKM 19.1) and 24 other tissues See more
Orthologs
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Genomic context

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Location:
4q27
Exon count:
14
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (121801323..121817021)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (125105375..125121073)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (122722478..122738176)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene annexin A5 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr4:122611545-122612744 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15659 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr4:122633152-122634351 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 15660 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr4:122669697-122670300 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr4:122670301-122670904 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_72694 Neighboring gene small integral membrane protein 43 Neighboring gene uncharacterized LOC100192379 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21868 Neighboring gene Sharpr-MPRA regulatory region 4891 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr4:122721667-122722470 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21870 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21871 Neighboring gene cyclin A2 Neighboring gene Bardet-Biedl syndrome 7 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 21872 Neighboring gene BBS7 divergent transcript

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
  • 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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Related articles in PubMed

  1. Novel EXOSC9 variants cause pontocerebellar hypoplasia type 1D with spinal motor neuronopathy and cerebellar atrophy. Sakamoto M, et al. J Hum Genet, 2021 Apr. PMID 33040083
  2. EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells. Yoshino S, et al. Sci Rep, 2020 Jun 9. PMID 32518284, Free PMC Article
  3. Expanded PCH1D phenotype linked to EXOSC9 mutation. Bizzari S, et al. Eur J Med Genet, 2020 Jan. PMID 30690203
  4. Molecular characterization of an autoantigen of PM-Scl in the polymyositis/scleroderma overlap syndrome: a unique and complete human cDNA encoding an apparent 75-kD acidic protein of the nucleolar complex. Alderuccio F, et al. J Exp Med, 1991 Apr 1. PMID 2007859, Free PMC Article
  5. Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy. Burns DT, et al. Am J Hum Genet, 2018 May 3. PMID 29727687, Free PMC Article

See all (103) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Exosc9 Initiates SUMO-Dependent lncRNA TERRA Degradation to Impact Telomeric Integrity in Endocrine Therapy Insensitive Hormone Receptor-Positive Breast Cancer.
    Title: Exosc9 Initiates SUMO-Dependent lncRNA TERRA Degradation to Impact Telomeric Integrity in Endocrine Therapy Insensitive Hormone Receptor-Positive Breast Cancer.
  2. Novel EXOSC9 variants cause pontocerebellar hypoplasia type 1D with spinal motor neuronopathy and cerebellar atrophy.
    Title: Novel EXOSC9 variants cause pontocerebellar hypoplasia type 1D with spinal motor neuronopathy and cerebellar atrophy.
  3. EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.
    Title: EXOSC9 depletion attenuates P-body formation, stress resistance, and tumorigenicity of cancer cells.
  4. Expanded PCH1D phenotype linked to EXOSC9 mutation.
    Title: Expanded PCH1D phenotype linked to EXOSC9 mutation.
  5. variants in EXOSC9 result in a neurological syndrome combining cerebellar atrophy and spinal motoneuronopathy, thus expanding the list of human exosomopathies.
    Title: Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy.
  6. Although not required for exosome stability, PM/Scl-100 and PM/Scl-75 are involved in mRNA degradation.
    Title: Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways.
  7. The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements, possibly by direct binding of PM/Scl-75 to these RNA regions.
    Title: The mammalian exosome mediates the efficient degradation of mRNAs that contain AU-rich elements.
  8. The association of the human PM/Scl-75 autoantigen with the exosome is dependent on a newly identified N terminus.
    Title: The association of the human PM/Scl-75 autoantigen with the exosome is dependent on a newly identified N terminus.
  9. PM-Scl-75 is the main autoantigen in patients with the polymyositis/scleroderma overlap syndrome.
    Title: PM-Scl-75 is the main autoantigen in patients with the polymyositis/scleroderma overlap syndrome.
  10. 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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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 1D
MedGen: C4748058 OMIM: 618065 GeneReviews: Not available
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Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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 NAS
Non-traceable Author Statement
more info
 PubMed 
enables RNA binding HDA PubMed 
enables RNA binding NAS
Non-traceable Author Statement
more info
 PubMed 
NOT enables RNA exonuclease activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables RNA polymerase II-specific DNA-binding transcription factor binding IEA
Inferred from Electronic Annotation
more info
  
enables mRNA 3'-UTR AU-rich region binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables mRNA 3'-UTR AU-rich region binding 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 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 U1 snRNA 3'-end processing 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 U5 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 immune response NAS
Non-traceable Author Statement
more info
 PubMed 
involved_in nuclear mRNA surveillance IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear mRNA surveillance 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 polyadenylation-dependent rRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in nuclear-transcribed mRNA 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, deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
  
involved_in rRNA processing NAS
Non-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 
located_in extracellular exosome HDA PubMed 
located_in nuclear chromosome IDA
Inferred from Direct Assay
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
 PubMed 
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 RRP45
Names
P75 polymyositis-scleroderma overlap syndrome associated autoantigen
PMSCL autoantigen, 75kD
autoantigen PM/Scl 1
exosome complex exonuclease RRP45
polymyositis/scleroderma autoantigen 1, 75kDa
NP_001029366.1
NP_005024.2
XP_011530337.1
XP_054206171.1

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

  1. NG_029848.1 RefSeqGene

    Range
    5007..20705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001034194.2 → NP_001029366.1  exosome complex component RRP45 isoform 1

    See identical proteins and their annotated locations for NP_001029366.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ517294, BU615347
    Consensus CDS
    CCDS34057.1
    UniProtKB/TrEMBL
    A5PLM5
    Related
    ENSP00000368984.3, ENST00000379663.7
    Conserved Domains (2) summary
    cd11368
    Location:6 → 264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10 → 271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]

  2. NM_005033.3 → NP_005024.2  exosome complex component RRP45 isoform 2

    See identical proteins and their annotated locations for NP_005024.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC079341
    Consensus CDS
    CCDS3722.2
    UniProtKB/Swiss-Prot
    Q06265, Q12883, Q4W5P5, Q86Y41, Q86Y48
    UniProtKB/TrEMBL
    A5PLM5
    Related
    ENSP00000243498.5, ENST00000243498.10
    Conserved Domains (2) summary
    cd11368
    Location:6 → 264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10 → 271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]

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

  1. NC_000004.12 Reference GRCh38.p14 Primary Assembly

    Range
    121801323..121817021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532035.4 → XP_011530337.1  exosome complex component RRP45 isoform X1

    See identical proteins and their annotated locations for XP_011530337.1

    UniProtKB/TrEMBL
    A5PLM5, B4DXG8
    Related
    ENST00000509980.5
    Conserved Domains (2) summary
    cd11368
    Location:6 → 264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10 → 271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]

RNA

  1. XR_007057929.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060928.1 Alternate T2T-CHM13v2.0

    Range
    125105375..125121073
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054350196.1 → XP_054206171.1  exosome complex component RRP45 isoform X1

    UniProtKB/TrEMBL
    B4DXG8

RNA

  1. XR_008486994.1 RNA Sequence

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q06265.3 GenPept UniProtKB/Swiss-Prot:Q06265

Gene LinkOut

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