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EXOSC3 exosome component 3 [ Homo sapiens (human) ]

Gene ID: 51010, updated on 3-May-2020

Summary

Official Symbol
EXOSC3provided by HGNC
Official Full Name
exosome component 3provided by HGNC
Primary source
HGNC:HGNC:17944
See related
Ensembl:ENSG00000107371 MIM:606489
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]
Expression
Ubiquitous expression in testis (RPKM 9.5), lymph node (RPKM 7.7) and 25 other tissues See more
Orthologs

Genomic context

See EXOSC3 in Genome Data Viewer
Location:
9p13.2
Exon count:
4
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 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 RN7SK pseudogene 171 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

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

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
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
CUT catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
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
 
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
PubMed 
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
PubMed 
nuclear polyadenylation-dependent tRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription 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 
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) IBA
Inferred from Biological aspect of Ancestor
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) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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 
nuclear exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
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 

General protein information

Preferred Names
exosome complex component RRP40
Names
exosome complex exonuclease RRP40
ribosomal RNA-processing protein 40

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.

Genomic

  1. NG_032780.1 RefSeqGene

    Range
    5029..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
    ENSP00000379775.3, ENST00000396521.3
    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_016042.4NP_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
    Consensus CDS
    CCDS35016.1
    UniProtKB/Swiss-Prot
    Q9NQT5
    Related
    ENSP00000323046.4, ENST00000327304.10
    Conserved Domains (2) summary
    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 ...
    cl26026
    Location:26274
    ECR1_N; Exosome complex exonuclease RRP4 N-terminal region

RefSeqs of Annotated Genomes: Homo sapiens Updated 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_000009.12 Reference GRCh38.p13 Primary Assembly

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