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EXOSC1 exosome component 1 [ Homo sapiens (human) ]

Gene ID: 51013, updated on 26-May-2016
Official Symbol
EXOSC1provided by HGNC
Official Full Name
exosome component 1provided by HGNC
Primary source
HGNC:HGNC:17286
See related
Ensembl:ENSG00000171311 HPRD:16223; MIM:606493; Vega:OTTHUMG00000018854
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; 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]
Orthologs
Location:
10q24
Exon count:
10
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 10 NC_000010.11 (97435909..97446011, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (99195666..99205808, complement)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene ribosomal RNA processing 12 homolog Neighboring gene uncharacterized LOC644215 Neighboring gene phosphoglycerate mutase 1 Neighboring gene zinc finger DHHC-type containing 16 Neighboring gene MMS19 homolog, cytosolic iron-sulfur assembly component

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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

  • 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, archaea, organism-specific biosystem (from KEGG)
    Exosome, archaea, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exosome, archaea, conserved biosystem (from KEGG)
    Exosome, archaea, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • 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, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus, 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...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
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
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
rRNA processing TAS
Traceable Author Statement
more info
 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
cytosol TAS
Traceable Author Statement
more info
 
exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
exosome (RNase complex) NAS
Non-traceable Author Statement
more info
PubMed 
nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
Preferred Names
exosome complex component CSL4
Names
3'-5' exoribonuclease CSL4 homolog
exosomal core protein CSL4
homolog of yeast exosomal core protein CSL4

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_001318362.1NP_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
    UniProtKB/Swiss-Prot
    Q9Y3B2
    UniProtKB/TrEMBL
    B1AMU3
    Conserved Domains (3) summary
    COG1096
    Location:10161
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    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_001318363.1NP_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
    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_001318364.1NP_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 (3) summary
    COG1096
    Location:10120
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    pfam14382
    Location:839
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region
    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. ...
  4. NM_001318365.1NP_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_001318366.1NP_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_016046.4NP_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, OTTHUMP00000020203, ENST00000370902, OTTHUMT00000049680
    Conserved Domains (3) summary
    COG1096
    Location:10186
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    cd05791
    Location:62154
    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

RNA

  1. NR_134586.1 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, BI550688, BU569997
  2. NR_134587.1 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 Annotation Release 107 details...

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

Reference GRCh38.p2 Primary Assembly

Genomic

  1. NC_000010.11 Reference GRCh38.p2 Primary Assembly

    Range
    97435909..97446011 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011539846.1XP_011538148.1  

    Related
    ENSP00000359922, OTTHUMP00000020205, ENST00000370885, OTTHUMT00000049687
    Conserved Domains (3) summary
    COG1096
    Location:10161
    Csl4; Exosome complex RNA-binding protein Csl4, contains S1 and Zn-ribbon domains [Translation, ribosomal structure and biogenesis]
    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. XM_011539847.1XP_011538149.1  

    Conserved Domains (1) summary
    cd05791
    Location:27119
    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 ...
  3. XM_011539845.1XP_011538147.1  

    Conserved Domains (2) summary
    cd05791
    Location:62134
    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

RNA

  1. XR_945768.1 RNA Sequence

  2. XR_246092.2 RNA Sequence

Alternate CHM1_1.1

Genomic

  1. NC_018921.2 Alternate CHM1_1.1

    Range
    99477406..99487508 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)