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EXOSC1 exosome component 1 [ Homo sapiens (human) ]

Gene ID: 51013, updated on 5-Sep-2021

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
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
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Genomic context

See EXOSC1 in Genome Data Viewer
Location:
10q24.1
Exon count:
9
Annotation release Status Assembly Chr Location
109.20210514 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (97435909..97446006, complement)
105.20201022 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 phosphoglycerate mutase 1 Neighboring gene zinc finger DHHC-type palmitoyltransferase 16 Neighboring gene MMS19 homolog, cytosolic iron-sulfur assembly component

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

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
NOT enables exoribonuclease 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 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
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
PubMed 
located_in nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 

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)

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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_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/Swiss-Prot
    Q9Y3B2
    UniProtKB/TrEMBL
    B1AMU3
    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/Swiss-Prot
    Q9Y3B2
    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
    Q9Y3B2
    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: Homo sapiens Updated Annotation Release 109.20210514

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_024448033.1XP_024303801.1  exosome complex component CSL4 isoform X3

    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. ...
  2. XM_017016304.1XP_016871793.1  exosome complex component CSL4 isoform X2

  3. XM_011539847.2XP_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 ...
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