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EXOSC3 exosome component 3 [ Homo sapiens (human) ]

Gene ID: 51010, updated on 26-May-2016
Official Symbol
EXOSC3provided by HGNC
Official Full Name
exosome component 3provided by HGNC
Primary source
HGNC:HGNC:17944
See related
Ensembl:ENSG00000107371 HPRD:16220; MIM:606489; Vega:OTTHUMG00000019932
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
p10; PCH1B; RRP40; Rrp40p; CGI-102; hRrp-40; bA3J10.7
Summary
This gene encodes a non-catalytic component of the human exosome, a complex with 3'-5' exoribonuclease activity that plays a role in numerous RNA processing and degradation activities. Related pseudogenes of this gene are found on chromosome 19 and 21. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jun 2012]
Orthologs
Location:
9p11
Exon count:
4
Annotation release Status Assembly Chr Location
107 current GRCh38.p2 (GCF_000001405.28) 9 NC_000009.12 (37779714..37785092, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (37779711..37785089, complement)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene FERM and PDZ domain containing 1 Neighboring gene RAB1C, member RAS oncogene family pseudogene Neighboring gene tRNA methyltransferase 10B Neighboring gene uncharacterized LOC105376037 Neighboring gene DDB1 and CUL4 associated factor 10 Neighboring gene mitochondrial ribosomal protein S10 pseudogene 5

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Replication interactions

Interaction Pubs
Knockdown of exosome component 3 (EXOSC3) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl cells 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, 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

Clone Names

  • MGC723, MGC15120

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5'-exoribonuclease activity NAS
Non-traceable Author Statement
more info
PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
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
CUT catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA deamination IDA
Inferred from Direct Assay
more info
PubMed 
U4 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
 
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
 
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
 
isotype switching ISS
Inferred from Sequence or Structural Similarity
more info
 
nuclear polyadenylation-dependent rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
nuclear polyadenylation-dependent tRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
 
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription IBA
Inferred from Biological aspect of Ancestor
more info
 
nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' IBA
Inferred from Biological aspect of Ancestor
more info
 
polyadenylation-dependent snoRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
 
positive regulation of isotype switching IEA
Inferred from Electronic Annotation
more info
 
rRNA processing IDA
Inferred from Direct Assay
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 IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic exosome (RNase complex) IDA
Inferred from Direct Assay
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) IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
transcriptionally active chromatin IMP
Inferred from Mutant Phenotype
more info
PubMed 
Preferred Names
exosome complex component RRP40
Names
exosome complex exonuclease RRP40
ribosomal RNA-processing protein 40

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.

Genomic

  1. NG_032780.1 RefSeqGene

    Range
    5001..10379
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001002269.2NP_001002269.1  exosome complex component RRP40 isoform 2

    See identical proteins and their annotated locations for NP_001002269.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region that causes a frameshift and leads to an early stop codon compared to variant 1. The resulting protein (isoform 2) is shorter and has a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF229833, AK290864, BE048144, BP237222, DA352003
    Consensus CDS
    CCDS43805.1
    UniProtKB/Swiss-Prot
    Q9NQT5
    UniProtKB/TrEMBL
    Q9NYS3
    Related
    ENSP00000379775, OTTHUMP00000215532, ENST00000396521, OTTHUMT00000052479
    Conserved Domains (1) summary
    cl09927
    Location:108159
    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. NM_016042.3NP_057126.2  exosome complex component RRP40 isoform 1

    See identical proteins and their annotated locations for NP_057126.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AF281132, AK290864, BE048144, BP237222
    Consensus CDS
    CCDS35016.1
    UniProtKB/Swiss-Prot
    Q9NQT5
    Related
    ENSP00000323046, OTTHUMP00000021392, ENST00000327304, OTTHUMT00000052478
    Conserved Domains (2) summary
    COG1097
    Location:26274
    Rrp4; Exosome complex RNA-binding protein Rrp4, contains S1 and KH domains [Translation, ribosomal structure and biogenesis]
    cd05790
    Location:108193
    S1_Rrp40; S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation ...

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_000009.12 Reference GRCh38.p2 Primary Assembly

    Range
    37779714..37785092 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018920.2 Alternate CHM1_1.1

    Range
    37781396..37786774 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)