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    EXOSC9 exosome component 9 [ Homo sapiens (human) ]

    Gene ID: 5393, updated on 2-Nov-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
    mouse all
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    Genomic context

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    See EXOSC9 in Genome Data Viewer
    Location:
    4q27
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 4 NC_000004.12 (121801323..121817021)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 4 NC_060928.1 (125105375..125121073)
    RS_2024_09 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 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. Exosc9 Initiates SUMO-Dependent lncRNA TERRA Degradation to Impact Telomeric Integrity in Endocrine Therapy Insensitive Hormone Receptor-Positive Breast Cancer. Quttina M, et al. Cells, 2023 Oct 20. PMID 37887339, Free PMC Article
    2. 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
    3. Expanded PCH1D phenotype linked to EXOSC9 mutation. Bizzari S, et al. Eur J Med Genet, 2020 Jan. PMID 30690203
    4. 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
    5. 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

    See all (117) 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
    		Compare labs

    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 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 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 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 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 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 
    NOT located_in nucleolus IDA
    Inferred from Direct Assay
    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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