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Aliases for EXOSC3 Gene

Aliases for EXOSC3 Gene

  • Exosome Component 3 2 3 4 5
  • Ribosomal RNA-Processing Protein 40 3 4
  • RRP40 3 4
  • P10 3 4
  • Exosome Complex Exonuclease RRP40 3
  • Exosome Component Rrp40 2
  • CGI-102 Protein 2
  • BA3J10.7 3
  • CGI-102 3
  • HRrp-40 3
  • Rrp40p 3
  • PCH1B 3

External Ids for EXOSC3 Gene

Previous GeneCards Identifiers for EXOSC3 Gene

  • GC09M037771

Summaries for EXOSC3 Gene

Entrez Gene Summary for EXOSC3 Gene

  • 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]

GeneCards Summary for EXOSC3 Gene

EXOSC3 (Exosome Component 3) is a Protein Coding gene. Diseases associated with EXOSC3 include Pontocerebellar Hypoplasia, Type 1B and Pontocerebellar Hypoplasia Type 1. Among its related pathways are Gene Expression and CDK-mediated phosphorylation and removal of Cdc6. GO annotations related to this gene include RNA binding and exoribonuclease activity.

UniProtKB/Swiss-Prot for EXOSC3 Gene

  • Non-catalytic component of the RNA exosome complex which has 3->5 exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding pervasive transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3 untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.

Gene Wiki entry for EXOSC3 Gene

No data available for Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EXOSC3 Gene

Genomics for EXOSC3 Gene

Regulatory Elements for EXOSC3 Gene

Enhancers for EXOSC3 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around EXOSC3 on UCSC Golden Path with GeneCards custom track

Genomic Location for EXOSC3 Gene

Chromosome:
9
Start:
37,766,978 bp from pter
End:
37,801,437 bp from pter
Size:
34,460 bases
Orientation:
Minus strand

Genomic View for EXOSC3 Gene

Genes around EXOSC3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXOSC3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXOSC3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXOSC3 Gene

Proteins for EXOSC3 Gene

  • Protein details for EXOSC3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NQT5-EXOS3_HUMAN
    Recommended name:
    Exosome complex component RRP40
    Protein Accession:
    Q9NQT5
    Secondary Accessions:
    • A8K0K6
    • Q5QP85
    • Q9Y3A8

    Protein attributes for EXOSC3 Gene

    Size:
    275 amino acids
    Molecular mass:
    29572 Da
    Quaternary structure:
    • Component of the RNA exosome complex. Specifically part of the catalytically inactive RNA exosome core (Exo-9) complex which is believed to associate with catalytic subunits EXOSC10, and DIS3 or DIS3L in cytoplasmic- and nuclear-specific RNA exosome complex forms. Exo-9 is formed by a hexameric ring of RNase PH domain-containing subunits specifically containing the heterodimers EXOSC4-EXOSC9, EXOSC5-EXOSC8 and EXOSC6-EXOSC7, and peripheral S1 domain-containing components EXOSC1, EXOSC2 and EXOSC3 located on the top of the ring structure. Interacts with GTPBP1. Interacts with ZC3HAV1. Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner.

    Three dimensional structures from OCA and Proteopedia for EXOSC3 Gene

    Alternative splice isoforms for EXOSC3 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EXOSC3 Gene

Proteomics data for EXOSC3 Gene at MOPED

Post-translational modifications for EXOSC3 Gene

  • Ubiquitination at Lys 113
  • Modification sites at PhosphoSitePlus

Other Protein References for EXOSC3 Gene

No data available for DME Specific Peptides for EXOSC3 Gene

Domains & Families for EXOSC3 Gene

Gene Families for EXOSC3 Gene

Protein Domains for EXOSC3 Gene

Suggested Antigen Peptide Sequences for EXOSC3 Gene

Graphical View of Domain Structure for InterPro Entry

Q9NQT5

UniProtKB/Swiss-Prot:

EXOS3_HUMAN :
  • Belongs to the RRP40 family.
Family:
  • Belongs to the RRP40 family.
genes like me logo Genes that share domains with EXOSC3: view

Function for EXOSC3 Gene

Molecular function for EXOSC3 Gene

UniProtKB/Swiss-Prot Function:
Non-catalytic component of the RNA exosome complex which has 3->5 exoribonuclease activity and participates in a multitude of cellular RNA processing and degradation events. In the nucleus, the RNA exosome complex is involved in proper maturation of stable RNA species such as rRNA, snRNA and snoRNA, in the elimination of RNA processing by-products and non-coding pervasive transcripts, such as antisense RNA species and promoter-upstream transcripts (PROMPTs), and of mRNAs with processing defects, thereby limiting or excluding their export to the cytoplasm. The RNA exosome may be involved in Ig class switch recombination (CSR) and/or Ig variable region somatic hypermutation (SHM) by targeting AICDA deamination activity to transcribed dsDNA substrates. In the cytoplasm, the RNA exosome complex is involved in general mRNA turnover and specifically degrades inherently unstable mRNAs containing AU-rich elements (AREs) within their 3 untranslated regions, and in RNA surveillance pathways, preventing translation of aberrant mRNAs. It seems to be involved in degradation of histone mRNA. The catalytic inactive RNA exosome core complex of 9 subunits (Exo-9) is proposed to play a pivotal role in the binding and presentation of RNA for ribonucleolysis, and to serve as a scaffold for the association with catalytic subunits and accessory proteins or complexes. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5.
genes like me logo Genes that share phenotypes with EXOSC3: view

Human Phenotype Ontology for EXOSC3 Gene

HPO Id HPO Name Alternative Ids Definition Synonyms

Animal Models for EXOSC3 Gene

MGI Knock Outs for EXOSC3:

Animal Model Products

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , miRNA , Transcription Factor Targets and HOMER Transcription for EXOSC3 Gene

Localization for EXOSC3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXOSC3 Gene

Cytoplasm. Nucleus, nucleolus. Nucleus.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for EXOSC3 Gene COMPARTMENTS Subcellular localization image for EXOSC3 gene
Compartment Confidence
cytosol 5
nucleus 5
mitochondrion 2
extracellular 1

Gene Ontology (GO) - Cellular Components for EXOSC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IDA 17545563
genes like me logo Genes that share ontologies with EXOSC3: view

Pathways & Interactions for EXOSC3 Gene

genes like me logo Genes that share pathways with EXOSC3: view

Pathways by source for EXOSC3 Gene

Gene Ontology (GO) - Biological Process for EXOSC3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing IDA,TAS --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
GO:0045830 positive regulation of isotype switching IEA --
GO:0071034 CUT catabolic process IMP 19056938
GO:0071038 nuclear polyadenylation-dependent tRNA catabolic process IBA --
genes like me logo Genes that share ontologies with EXOSC3: view

No data available for SIGNOR curated interactions for EXOSC3 Gene

Drugs & Compounds for EXOSC3 Gene

No Compound Related Data Available

Transcripts for EXOSC3 Gene

Unigene Clusters for EXOSC3 Gene

Exosome component 3:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for EXOSC3 Gene

ExUns: 1a · 1b ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c
SP1: - -
SP2: - - -
SP3: -
SP4: - -

Relevant External Links for EXOSC3 Gene

GeneLoc Exon Structure for
EXOSC3
ECgene alternative splicing isoforms for
EXOSC3

Expression for EXOSC3 Gene

mRNA expression in normal human tissues for EXOSC3 Gene

Protein differential expression in normal tissues from HIPED for EXOSC3 Gene

This gene is overexpressed in Breast (8.7) and Pancreas (8.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for EXOSC3 Gene



SOURCE GeneReport for Unigene cluster for EXOSC3 Gene Hs.602571

genes like me logo Genes that share expression patterns with EXOSC3: view

Protein tissue co-expression partners for EXOSC3 Gene

- Elite partner

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt for EXOSC3 Gene

Orthologs for EXOSC3 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EXOSC3 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia EXOSC3 35
  • 89.33 (n)
  • 94.18 (a)
EXOSC3 36
  • 94 (a)
OneToOne
dog
(Canis familiaris)
Mammalia EXOSC3 35
  • 90.67 (n)
  • 92.73 (a)
EXOSC3 36
  • 92 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Exosc3 35
  • 84.67 (n)
  • 87.59 (a)
Exosc3 16
Exosc3 36
  • 88 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia EXOSC3 35
  • 99.15 (n)
  • 98.91 (a)
EXOSC3 36
  • 99 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Exosc3 35
  • 85.58 (n)
  • 86.54 (a)
oppossum
(Monodelphis domestica)
Mammalia EXOSC3 36
  • 83 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EXOSC3 36
  • 73 (a)
OneToOne
chicken
(Gallus gallus)
Aves EXOSC3 35
  • 70.18 (n)
  • 73.05 (a)
EXOSC3 36
  • 71 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EXOSC3 36
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia LOC100491278 35
  • 68.71 (n)
  • 69.39 (a)
Str.7004 35
African clawed frog
(Xenopus laevis)
Amphibia Xl.24761 35
zebrafish
(Danio rerio)
Actinopterygii exosc3 35
  • 66.23 (n)
  • 67.25 (a)
exosc3 36
  • 61 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP010247 35
  • 55.05 (n)
  • 45.96 (a)
fruit fly
(Drosophila melanogaster)
Insecta Rrp40 35
  • 52.2 (n)
  • 48.68 (a)
Rrp40 36
  • 43 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea exos-3 35
  • 48.78 (n)
  • 40 (a)
exos-3 36
  • 38 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ADL196W 35
  • 47.14 (n)
  • 36.72 (a)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0E02091g 35
  • 48.13 (n)
  • 35.96 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP40 35
  • 46.99 (n)
  • 36.61 (a)
RRP40 36
  • 32 (a)
OneToOne
RRP40 38
thale cress
(Arabidopsis thaliana)
eudicotyledons AT2G25355 35
  • 49.17 (n)
  • 40 (a)
rice
(Oryza sativa)
Liliopsida Os01g0661400 35
  • 50.83 (n)
  • 40 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00693 35
  • 46.47 (n)
  • 36.45 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPAC22A12.12c 35
  • 49.65 (n)
  • 35.94 (a)
Species with no ortholog for EXOSC3:
  • Actinobacteria (Mycobacterium tuberculosis)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)

Evolution for EXOSC3 Gene

ENSEMBL:
Gene Tree for EXOSC3 (if available)
TreeFam:
Gene Tree for EXOSC3 (if available)

Paralogs for EXOSC3 Gene

(1) SIMAP similar genes for EXOSC3 Gene using alignment to 1 proteins:

Pseudogenes.org Pseudogenes for EXOSC3 Gene

genes like me logo Genes that share paralogs with EXOSC3: view

No data available for Paralogs for EXOSC3 Gene

Variants for EXOSC3 Gene

Sequence variations from dbSNP and Humsavar for EXOSC3 Gene

SNP ID Clin Chr 09 pos Sequence Context AA Info Type
rs3208406 - 37,780,834(+) TGGAT(A/G)GAGTT reference, missense, utr-variant-3-prime
VAR_068505 Pontocerebellar hypoplasia 1B (PCH1B)
rs141138948 Pontocerebellar hypoplasia 1B (PCH1B) 37,783,993(+) CAACA(G/T)CAACT reference, missense
VAR_068507 Pontocerebellar hypoplasia 1B (PCH1B)
VAR_068508 Pontocerebellar hypoplasia 1B (PCH1B)

Structural Variations from Database of Genomic Variants (DGV) for EXOSC3 Gene

Variant ID Type Subtype PubMed ID
nsv831552 CNV Gain 17160897
nsv893062 CNV Gain 21882294
nsv469814 CNV Gain 16826518

Variation tolerance for EXOSC3 Gene

Residual Variation Intolerance Score: 80.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.91; 59.38% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EXOSC3 Gene

Human Gene Mutation Database (HGMD)
EXOSC3

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXOSC3 Gene

Disorders for EXOSC3 Gene

MalaCards: The human disease database

(4) MalaCards diseases for EXOSC3 Gene - From: OMIM, ClinVar, GeneTests, Orphanet, Swiss-Prot, DISEASES, and GeneCards

Disorder Aliases PubMed IDs
pontocerebellar hypoplasia, type 1b
  • pontocerebellar hypoplasia type 1b
pontocerebellar hypoplasia type 1
  • pontocerebellar hypoplasia with anterior horn cell disease
pontocerebellar hypoplasia
  • pch
exosc3-related pontocerebellar hypoplasia
  • pontocerebellar hypoplasia type 1b
- elite association - COSMIC cancer census association via MalaCards

UniProtKB/Swiss-Prot

EXOS3_HUMAN
  • Pontocerebellar hypoplasia 1B (PCH1B) [MIM:614678]: A severe autosomal recessive neurologic disorder characterized by a combination of cerebellar and spinal motor neuron degeneration beginning at birth. There is diffuse muscle weakness, progressive microcephaly, global developmental delay, and brainstem involvement. {ECO:0000269 PubMed:22544365}. Note=The disease is caused by mutations affecting the gene represented in this entry.

Relevant External Links for EXOSC3

Genetic Association Database (GAD)
EXOSC3
Human Genome Epidemiology (HuGE) Navigator
EXOSC3
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EXOSC3
genes like me logo Genes that share disorders with EXOSC3: view

No data available for Genatlas for EXOSC3 Gene

Publications for EXOSC3 Gene

  1. Three novel components of the human exosome. (PMID: 11110791) Brouwer R. … Pruijn G.J.M. (J. Biol. Chem. 2001) 2 3 4 67
  2. Identification of novel human genes evolutionarily conserved in Caenorhabditis elegans by comparative proteomics. (PMID: 10810093) Lai C.-H. … Lin W.-C. (Genome Res. 2000) 2 3
  3. Interactions of the Antiviral Factor Interferon Gamma-Inducible Protein 16 (IFI16) Mediate Immune Signaling and Herpes Simplex Virus-1 Immunosuppression. (PMID: 25693804) Diner B.A. … Cristea I.M. (Mol. Cell Proteomics 2015) 3
  4. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3
  5. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3

Products for EXOSC3 Gene

Sources for EXOSC3 Gene

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