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    EXOSC3 exosome component 3 [ Homo sapiens (human) ]

    Gene ID: 51010, updated on 5-Mar-2024

    Summary

    Official Symbol
    EXOSC3provided by HGNC
    Official Full Name
    exosome component 3provided by HGNC
    Primary source
    HGNC:HGNC:17944
    See related
    Ensembl:ENSG00000107371 MIM:606489; AllianceGenome:HGNC:17944
    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
    p10; PCH1B; RRP40; Rrp40p; CGI-102; hRrp-40; bA3J10.7
    Summary
    This gene encodes a non-catalytic component of the human exosome, a complex with 3'-5' exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2012]
    Expression
    Ubiquitous expression in testis (RPKM 9.5), lymph node (RPKM 7.7) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See EXOSC3 in Genome Data Viewer
    Location:
    9p13.2
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (37779714..37785092, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (37803445..37808823, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37779711..37785089, complement)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene FERM and PDZ domain containing 1 Neighboring gene RN7SK pseudogene 171 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:37697369-37697615 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:37745887-37746388 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:37753712-37753946 Neighboring gene tRNA methyltransferase 10B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28402 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:37784801-37785316 Neighboring gene uncharacterized LOC105376037 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:37800323-37800924 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19913 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28404 Neighboring gene DDB1 and CUL4 associated factor 10 Neighboring gene mitochondrial ribosomal protein S10 pseudogene 5

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of exosome component 3 (EXOSC3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • MGC723, MGC15120

    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 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 CUT catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in DNA deamination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    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 U4 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in exonucleolytic catabolism of deadenylated mRNA IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in exonucleolytic catabolism of deadenylated mRNA IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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 isotype switching ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in nuclear polyadenylation-dependent rRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear polyadenylation-dependent tRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in polyadenylation-dependent snoRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of isotype switching IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in rRNA processing 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) IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of cytoplasmic exosome (RNase complex) 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 
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    part_of euchromatin IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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

    Preferred Names
    exosome complex component RRP40
    Names
    exosome complex exonuclease RRP40
    ribosomal RNA-processing protein 40

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_032780.1 RefSeqGene

      Range
      5029..10379
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001002269.2NP_001002269.1  exosome complex component RRP40 isoform 2

      See identical proteins and their annotated locations for NP_001002269.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the coding region that causes a frameshift and leads to an early stop codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
      Source sequence(s)
      AF229833, AK290864, BE048144, BP237222, DA352003
      Consensus CDS
      CCDS43805.1
      UniProtKB/Swiss-Prot
      Q9NQT5
      UniProtKB/TrEMBL
      Q9NYS3
      Related
      ENSP00000379775.3, ENST00000396521.3
      Conserved Domains (1) summary
      cl09927
      Location:108159
      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. ...
    2. NM_016042.4NP_057126.2  exosome complex component RRP40 isoform 1

      See identical proteins and their annotated locations for NP_057126.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AF281132, AK290864, BE048144
      Consensus CDS
      CCDS35016.1
      UniProtKB/Swiss-Prot
      A8K0K6, Q5QP85, Q9NQT5, Q9Y3A8
      Related
      ENSP00000323046.4, ENST00000327304.10
      Conserved Domains (2) summary
      cd05790
      Location:108193
      S1_Rrp40; S1_Rrp40: Rrp40 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 ...
      cl26026
      Location:26274
      ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      37779714..37785092 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      37803445..37808823 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)