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    EXOSC1 exosome component 1 [ Homo sapiens (human) ]

    Gene ID: 51013, updated on 7-Jul-2024

    Summary

    Official Symbol
    EXOSC1provided by HGNC
    Official Full Name
    exosome component 1provided by HGNC
    Primary source
    HGNC:HGNC:17286
    See related
    Ensembl:ENSG00000171311 MIM:606493; AllianceGenome:HGNC:17286
    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
    p13; CSL4; SKI4; Csl4p; PCH1F; Ski4p; CGI-108
    Summary
    This gene encodes a core component of the exosome. The mammalian exosome is required for rapid degradation of AU rich element-containing RNAs but not for poly(A) shortening. The association of this protein with the exosome is mediated by protein-protein interactions with ribosomal RNA-processing protein 42 and ribosomal RNA-processing protein 46. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2016]
    Expression
    Ubiquitous expression in lymph node (RPKM 9.3), urinary bladder (RPKM 7.6) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See EXOSC1 in Genome Data Viewer
    Location:
    10q24.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 10 NC_000010.11 (97435909..97446006, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 10 NC_060934.1 (98316090..98326186, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (99195666..99205763, complement)

    Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC644215 Neighboring gene Sharpr-MPRA regulatory region 6385 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2677 Neighboring gene ReSE screen-validated silencer GRCh37_chr10:99186899-99187121 Neighboring gene phosphoglycerate mutase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:99204892-99205472 Neighboring gene H3K27ac hESC enhancer GRCh37_chr10:99205473-99206052 Neighboring gene zinc finger DHHC-type palmitoyltransferase 16 Neighboring gene MMS19 homolog, cytosolic iron-sulfur assembly component Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr10:99257304-99257834 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 3852 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 2679

    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

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, exosome component 1 (EXOSC1), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with EXOSC1 is increased by RRE 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

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    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 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 rRNA processing IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    is_active_in cytoplasm 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 
    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 
    located_in nucleolus 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

    Preferred Names
    exosome complex component CSL4
    Names
    3'-5' exoribonuclease CSL4 homolog
    exosomal core protein CSL4
    homolog of yeast exosomal core protein CSL4

    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.

    mRNA and Protein(s)

    1. NM_001318362.2NP_001305291.1  exosome complex component CSL4 isoform b

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
      Source sequence(s)
      AF151866, AW954858, BI550688
      Consensus CDS
      CCDS81492.1
      UniProtKB/TrEMBL
      B1AMU3, B1AMU4
      Related
      ENSP00000359922.4, ENST00000370885.8
      Conserved Domains (2) summary
      cd05791
      Location:48129
      S1_CSL4; S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation ...
      pfam14382
      Location:839
      ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    2. NM_001318363.2NP_001305292.1  exosome complex component CSL4 isoform c

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate splice site and lacks two alternate in-frame exons in the 3' coding region, compared to variant 1, resulting in an isoform (c) that is shorter than isoform a.
      Source sequence(s)
      AF151866, BC022067, BI550688, N34159
      UniProtKB/TrEMBL
      R4GMQ7
      Related
      ENSP00000473660.1, ENST00000485122.6
      Conserved Domains (2) summary
      pfam14382
      Location:839
      ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
      cl09927
      Location:62116
      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. ...
    3. NM_001318364.2NP_001305293.1  exosome complex component CSL4 isoform d

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks three alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The encoded isoform (d) is shorter than isoform a.
      Source sequence(s)
      AF151866, BI550688, W39427
      UniProtKB/Swiss-Prot
      Q9Y3B2
      Conserved Domains (2) summary
      cl09927
      Location:4488
      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. ...
      cl26026
      Location:10120
      ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    4. NM_001318365.2NP_001305294.1  exosome complex component CSL4 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) includes an additional exon and uses an alternate splice site, and it thus differs in its 5' UTR and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.
      Source sequence(s)
      AF151866, BG331954, BI550688
      UniProtKB/Swiss-Prot
      Q9Y3B2
      Conserved Domains (1) summary
      cl09927
      Location:2968
      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. ...
    5. NM_001318366.2NP_001305295.1  exosome complex component CSL4 isoform e

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice site, and it thus differs in its 5' UTR and initiates translation from an alternate start codon, compared to variant 1. The encoded isoform (e) has a distinct and shorter N-terminus, compared to isoform a. Both variants 5 and 6 encode isoform e.
      Source sequence(s)
      AF151866, BI550688, BM692452
      UniProtKB/Swiss-Prot
      Q9Y3B2
      Conserved Domains (1) summary
      cl09927
      Location:2968
      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. ...
    6. NM_016046.5NP_057130.1  exosome complex component CSL4 isoform a

      See identical proteins and their annotated locations for NP_057130.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (a).
      Source sequence(s)
      AF151866, BC022067, BI550688
      Consensus CDS
      CCDS7459.1
      UniProtKB/Swiss-Prot
      B2R9B3, Q5JTH3, Q9Y3B2
      UniProtKB/TrEMBL
      B1AMU4
      Related
      ENSP00000359939.3, ENST00000370902.8
      Conserved Domains (2) summary
      cd05791
      Location:62154
      S1_CSL4; CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...
      pfam14382
      Location:839
      ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

    RNA

    1. NR_134586.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) lacks an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF151866, BU569997
    2. NR_134587.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (8) lacks two alternate internal exons and uses an alternate splice site in the 3' terminal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AF151866, AK307229, BI550688

    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_000010.11 Reference GRCh38.p14 Primary Assembly

      Range
      97435909..97446006 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011539847.3XP_011538149.1  exosome complex component CSL4 isoform X1

      Conserved Domains (1) summary
      cd05791
      Location:27119
      S1_CSL4; CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060934.1 Alternate T2T-CHM13v2.0

      Range
      98316090..98326186 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054365975.1XP_054221950.1  exosome complex component CSL4 isoform X1