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    EXOSC5 exosome component 5 [ Homo sapiens (human) ]

    Gene ID: 56915, updated on 17-Jun-2019

    Summary

    Official Symbol
    EXOSC5provided by HGNC
    Official Full Name
    exosome component 5provided by HGNC
    Primary source
    HGNC:HGNC:24662
    See related
    Ensembl:ENSG00000077348 MIM:606492
    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
    p12B; RRP46; RRP41B; Rrp46p; hRrp46p
    Expression
    Ubiquitous expression in lymph node (RPKM 8.8), ovary (RPKM 8.2) and 25 other tissues See more
    Orthologs

    Genomic context

    See EXOSC5 in Genome Data Viewer
    Location:
    19q13.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 19 NC_000019.10 (41386374..41397359, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 19 NC_000019.9 (41892275..41903289, complement)

    Chromosome 19 - NC_000019.10Genomic Context describing neighboring genes Neighboring gene transforming growth factor beta 1 Neighboring gene B9 domain containing 2 Neighboring gene transmembrane protein 91 Neighboring gene branched chain keto acid dehydrogenase E1 subunit alpha Neighboring gene UDP-GlcNAc:betaGal beta-1,3-N-acetylglucosaminyltransferase 8

    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 FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of exosome component 5 (EXOSC5) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells PubMed
    Knockdown of exosome component 5 (EXOSC5) by shRNA library screening inhibits HIV-1 replication in cultured Jurkat T-cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Pr55(Gag) gag Knockdown of exosome component 5 (EXOSC5) affects HIV-1 Gag trafficking, leading to inhibit HIV-1 replication in Jurkat cells PubMed
    Rev rev HIV-1 Rev interacting protein, exosome component 5 (EXOSC5), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EXOSC5 is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • ATF4 activates genes, organism-specific biosystem (from REACTOME)
      ATF4 activates genes, organism-specific biosystemATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
    • Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
      Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystemButyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the...
    • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
      Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
    • Exosome, eukaryotes, organism-specific biosystem (from KEGG)
      Exosome, eukaryotes, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
    • Exosome, eukaryotes, conserved biosystem (from KEGG)
      Exosome, eukaryotes, conserved biosystemStructural complex; Genetic information processing; RNA processing
    • Gene Expression, organism-specific biosystem (from REACTOME)
      Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
    • KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
      KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystemKSRP binds to AU-rich sequences in the 3' untranslated regions of mRNAs. KSRP causes the bound mRNA to be targeted for hydrolysis by recruiting exonucleases and decapping enzymes. The activity of KSR...
    • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
      Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
    • Metabolism of proteins, organism-specific biosystem (from REACTOME)
      Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
    • PERK regulates gene expression, organism-specific biosystem (from REACTOME)
      PERK regulates gene expression, organism-specific biosystemPERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintaine...
    • RNA degradation, organism-specific biosystem (from KEGG)
      RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
    • RNA degradation, conserved biosystem (from KEGG)
      RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
    • Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystem (from REACTOME)
      Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystemRNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-eleme...
    • Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
      Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystemTristetraproline (TTP) binds RNAs that contain AU-rich elements and recruits enzymes that degrade RNA. TTP interacts with the exosome (3' to 5' exonuclease), XRN1 (5' to 3' exonuclease), and the deca...
    • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
      Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...
    • mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystem (from REACTOME)
      mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystemThe degradation of mRNA from 3' to 5' occurs in two steps. First, the exosome exoribonuclease complex binds the 3' end of the oligoadenylated mRNA and hydrolyzes it from 3' to 5', yielding ribonucleo...
    • rRNA processing, organism-specific biosystem (from REACTOME)
      rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
    • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
      rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Homology

    Clone Names

    • MGC12901, MGC111224

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    3'-5'-exoribonuclease activity NAS
    Non-traceable Author Statement
    more info
    PubMed 
    RNA binding IEA
    Inferred from Electronic Annotation
    more info
     
    NOT exoribonuclease activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    DNA deamination IDA
    Inferred from Direct Assay
    more info
    PubMed 
    RNA phosphodiester bond hydrolysis, exonucleolytic IEA
    Inferred from Electronic Annotation
    more info
     
    U4 snRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    defense response to virus IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
    Traceable Author Statement
    more info
     
    nuclear mRNA surveillance IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    polyadenylation-dependent snoRNA 3'-end processing IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    rRNA catabolic process IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    rRNA processing NAS
    Non-traceable Author Statement
    more info
    PubMed 
    rRNA processing TAS
    Traceable Author Statement
    more info
     
    regulation of mRNA stability TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    cytoplasm NAS
    Non-traceable Author Statement
    more info
    PubMed 
    cytoplasmic exosome (RNase complex) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    exosome (RNase complex) IDA
    Inferred from Direct Assay
    more info
    PubMed 
    nuclear exosome (RNase complex) IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    nucleolus IDA
    Inferred from Direct Assay
    more info
     
    nucleolus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    nucleoplasm TAS
    Traceable Author Statement
    more info
     
    nucleus IDA
    Inferred from Direct Assay
    more info
     
    transcriptionally active chromatin IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 

    General protein information

    Preferred Names
    exosome complex component RRP46
    Names
    chronic myelogenous leukemia tumor antigen 28
    exosome complex exonuclease RRP46
    exosome component Rrp46
    ribosomal RNA-processing protein 46

    NCBI Reference Sequences (RefSeq)

    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_020158.4NP_064543.3  exosome complex component RRP46

      See identical proteins and their annotated locations for NP_064543.3

      Status: VALIDATED

      Source sequence(s)
      AC011462, AF281134
      Consensus CDS
      CCDS12580.1
      UniProtKB/Swiss-Prot
      Q9NQT4
      Related
      ENSP00000221233.3, ENST00000221233.9
      Conserved Domains (2) summary
      TIGR02065
      Location:28232
      ECX1; archaeal exosome-like complex exonuclease 1
      cd11372
      Location:28225
      RNase_PH_RRP46; RRP46 subunit of eukaryotic exosome

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000019.10 Reference GRCh38.p13 Primary Assembly

      Range
      41386374..41397359 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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