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    EXOSC4 exosome component 4 [ Homo sapiens (human) ]

    Gene ID: 54512, updated on 3-Nov-2024

    Summary

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    Official Symbol
    EXOSC4provided by HGNC
    Official Full Name
    exosome component 4provided by HGNC
    Primary source
    HGNC:HGNC:18189
    See related
    Ensembl:ENSG00000178896 MIM:606491; AllianceGenome:HGNC:18189
    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
    SKI6; p12A; RRP41; Ski6p; RRP41A; Rrp41p; hRrp41p
    Summary
    Enables mRNA 3'-UTR AU-rich region binding activity. Involved in several processes, including DNA deamination; maturation of 5.8S rRNA; and nuclear-transcribed mRNA catabolic process. Acts upstream of or within defense response to virus. Located in cytosol; euchromatin; and nucleoplasm. Part of exosome (RNase complex) and nucleolus. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in testis (RPKM 19.8), kidney (RPKM 7.7) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See EXOSC4 in Genome Data Viewer
    Location:
    8q24.3
    Exon count:
    4
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144064056..144080648)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145239523..145241499)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145133575..145135551)

    Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124902039 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145106761-145107658 Neighboring gene 5-oxoprolinase, ATP-hydrolysing Neighboring gene H3K27ac hESC enhancer GRCh37_chr8:145115803-145116323 Neighboring gene microRNA 6846 Neighboring gene uncharacterized LOC124902038 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28086 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28087 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19654 Neighboring gene microRNA 6847 Neighboring gene glycosylphosphatidylinositol anchor attachment 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145144930-145145430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145145431-145145931 Neighboring gene Sharpr-MPRA regulatory region 12380 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145150053-145150248 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28088 Neighboring gene cytochrome c1

    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. EXOSC4 functions as a potential oncogene in development and progression of colorectal cancer. Pan Y, et al. Mol Carcinog, 2018 Dec. PMID 30155936
    2. RUNX3 exerts tumor-suppressive role through inhibiting EXOSC4 expression. Wang N, et al. Funct Integr Genomics, 2024 May 17. PMID 38913281
    3. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival. Taniue K, et al. Int J Mol Sci, 2022 Jan 2. PMID 35008922, Free PMC Article
    4. Sequence-specific RNA binding mediated by the RNase PH domain of components of the exosome. Anderson JR, et al. RNA, 2006 Oct. PMID 16912217, Free PMC Article
    5. Osteopetrosis-Associated Transmembrane Protein 1 Recruits RNA Exosome To Restrict Hepatitis B Virus Replication. Ma C, et al. J Virol, 2020 May 18. PMID 32188736, Free PMC Article

    See all (115) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. RUNX3 exerts tumor-suppressive role through inhibiting EXOSC4 expression.
      Title: RUNX3 exerts tumor-suppressive role through inhibiting EXOSC4 expression.
    2. RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival.
      Title: RNA Exosome Component EXOSC4 Amplified in Multiple Cancer Types Is Required for the Cancer Cell Survival.
    3. Findings show that EXOSC4 is highly expressed in colorectal cancer (CRC) tumors and cell lines and demonstrate its oncogenic role in development and progression of CRC.
      Title: EXOSC4 functions as a potential oncogene in development and progression of colorectal cancer.
    4. 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.
    5. 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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    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

    Clone Names

    • FLJ20591

    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 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 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
    		  
    acts_upstream_of_or_within defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in histone mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in maturation of 5.8S rRNA 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-transcribed mRNA catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 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 
    located_in cytoplasm NAS
    Non-traceable Author Statement
    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
    		  
    located_in 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 
    located_in intracellular membrane-bounded organelle IDA
    Inferred from Direct Assay
    more info
    		  
    part_of nuclear exosome (RNase complex) IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    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 
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in nucleolus NAS
    Non-traceable Author Statement
    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 RRP41
    Names
    exosome complex exonuclease RRP41
    exosome component Rrp41
    ribosomal RNA-processing protein 41

    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_019037.3 → NP_061910.1  exosome complex component RRP41

      See identical proteins and their annotated locations for NP_061910.1

      Status: VALIDATED

      Source sequence(s)
      AK000598, BC002777, BM839994
      Consensus CDS
      CCDS6414.1
      UniProtKB/Swiss-Prot
      Q9NPD3
      Related
      ENSP00000315476.4, ENST00000316052.6
      Conserved Domains (1) summary
      cd11370
      Location:11 → 237
      RNase_PH_RRP41; RRP41 subunit of eukaryotic exosome

    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_000008.11 Reference GRCh38.p14 Primary Assembly

      Range
      144064056..144080648
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011517134.4 → XP_011515436.1  exosome complex component RRP41 isoform X1

      Conserved Domains (1) summary
      cl03114
      Location:1 → 139
      RNase_PH; RNase PH-like 3'-5' exoribonucleases

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060932.1 Alternate T2T-CHM13v2.0

      Range
      145239523..145241499
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NPD3.3 GenPept UniProtKB/Swiss-Prot:Q9NPD3

    Gene LinkOut

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

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