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Aliases for EXOSC4 Gene

Aliases for EXOSC4 Gene

  • Exosome Component 4 2 3 4 5
  • Ribosomal RNA-Processing Protein 41 3 4
  • Exosome Component Rrp41 2 3
  • RRP41 3 4
  • SKI6 3 4
  • P12A 3 4
  • Exosome Complex Exonuclease RRP41 3
  • Exosome Complex Component RRP41 3
  • HRrp41p 3
  • RRP41A 3
  • Rrp41p 3
  • Ski6p 3

External Ids for EXOSC4 Gene

Previous GeneCards Identifiers for EXOSC4 Gene

  • GC08P145240
  • GC08P145205
  • GC08P145133
  • GC08P140409

Summaries for EXOSC4 Gene

GeneCards Summary for EXOSC4 Gene

EXOSC4 (Exosome Component 4) is a Protein Coding gene. Among its related pathways are Regulation of activated PAK-2p34 by proteasome mediated degradation and Purine metabolism (KEGG). GO annotations related to this gene include 3-5-exoribonuclease activity and exoribonuclease activity. An important paralog of this gene is EXOSC6.

UniProtKB/Swiss-Prot for EXOSC4 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. EXOSC4 binds to ARE-containing RNAs.

Gene Wiki entry for EXOSC4 Gene

No data available for Entrez Gene Summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EXOSC4 Gene

Genomics for EXOSC4 Gene

Regulatory Elements for EXOSC4 Gene

Enhancers for EXOSC4 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH08F143968 1.4 Ensembl ENCODE 11.4 -89.8 -89848 11.0 HDGF PKNOX1 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 PLEC GPAA1 MAF1 WDR97 C8orf82 ZNF251 LRRC14 ZNF623 ZNF250 MIR661
GH08F143964 1.2 FANTOM5 Ensembl ENCODE 11.5 -97.9 -97940 3.6 PKNOX1 HLF SIN3A MNT CEBPG ZNF592 HIC1 CTBP1 GATA3 GLIS1 PLEC PARP10 SPATC1 EXOSC4 ENSG00000255224 MIR6847 EPPK1 PUF60 C8orf82 C8orf31
GH08F144002 1.1 Ensembl ENCODE 11.8 -59.6 -59584 3.5 HDAC1 PKNOX1 SAP130 MAX CEBPG THRB RAD21 YY1 GATA3 SCRT2 PLEC WDR97 EXOSC4 ENSG00000255224 MIR6847 MIR661 GPAA1 CYC1 MAF1 SHARPIN
GH08F143960 1 Ensembl ENCODE 11.5 -102.0 -101987 4.2 SOX13 SAP130 MAX ZNF644 RAD21 TEAD3 ZNF316 GATA3 ZNF766 NFE2 PLEC SPATC1 PARP10 EXOSC4 ENSG00000255224 MIR6847 EPPK1 PUF60 C8orf31 BOP1
GH08F143905 0.9 ENCODE 10.8 -157.8 -157829 1.5 HDAC1 ELF3 TBP ARID4B DMAP1 ZNF48 RAD21 RARA SLC30A9 CBX5 PLEC EPPK1 PUF60 MIR661 NRBP2 MIR6845 MIR937 SCRIB SPATC1 PARP10
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EXOSC4 on UCSC Golden Path with GeneCards custom track

Genomic Location for EXOSC4 Gene

Chromosome:
8
Start:
144,064,087 bp from pter
End:
144,080,648 bp from pter
Size:
16,562 bases
Orientation:
Plus strand

Genomic View for EXOSC4 Gene

Genes around EXOSC4 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXOSC4 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXOSC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXOSC4 Gene

Proteins for EXOSC4 Gene

  • Protein details for EXOSC4 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9NPD3-EXOS4_HUMAN
    Recommended name:
    Exosome complex component RRP41
    Protein Accession:
    Q9NPD3

    Protein attributes for EXOSC4 Gene

    Size:
    245 amino acids
    Molecular mass:
    26383 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 DDX60.
    • 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 DDX60.

    Three dimensional structures from OCA and Proteopedia for EXOSC4 Gene

neXtProt entry for EXOSC4 Gene

Post-translational modifications for EXOSC4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EXOSC4 Gene

Antibody Products

  • Abcam antibodies for EXOSC4
  • Santa Cruz Biotechnology (SCBT) Antibodies for EXOSC4

No data available for DME Specific Peptides for EXOSC4 Gene

Domains & Families for EXOSC4 Gene

Gene Families for EXOSC4 Gene

Suggested Antigen Peptide Sequences for EXOSC4 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9NPD3

UniProtKB/Swiss-Prot:

EXOS4_HUMAN :
  • Belongs to the RNase PH family.
Family:
  • Belongs to the RNase PH family.
genes like me logo Genes that share domains with EXOSC4: view

Function for EXOSC4 Gene

Molecular function for EXOSC4 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. EXOSC4 binds to ARE-containing RNAs.

Gene Ontology (GO) - Molecular Function for EXOSC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3-5-exoribonuclease activity NAS 11110791
GO:0003723 RNA binding IEA --
GO:0004532 NOT exoribonuclease activity IDA 17174896
GO:0005515 protein binding IPI 11719186
GO:0017091 AU-rich element binding IDA 16912217
genes like me logo Genes that share ontologies with EXOSC4: view
genes like me logo Genes that share phenotypes with EXOSC4: view

Animal Model Products

  • Taconic Biosciences Mouse Models for EXOSC4

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EXOSC4 Gene

Localization for EXOSC4 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXOSC4 Gene

Cytoplasm. Nucleus, nucleolus. Nucleus.

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for EXOSC4 gene
Compartment Confidence
cytoskeleton 5
nucleus 5
cytosol 5
extracellular 2
peroxisome 2

Gene Ontology (GO) - Cellular Components for EXOSC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 nuclear exosome (RNase complex) IBA --
GO:0000177 cytoplasmic exosome (RNase complex) IBA --
GO:0000178 exosome (RNase complex) IEA,IDA 20531389
GO:0005634 nucleus IEA,IDA 17545563
GO:0005654 nucleoplasm TAS --
genes like me logo Genes that share ontologies with EXOSC4: view

Pathways & Interactions for EXOSC4 Gene

genes like me logo Genes that share pathways with EXOSC4: view

Pathways by source for EXOSC4 Gene

Gene Ontology (GO) - Biological Process for EXOSC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000460 maturation of 5.8S rRNA IMP 20368444
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 17545563
GO:0006364 rRNA processing TAS --
GO:0016075 rRNA catabolic process IBA --
GO:0030307 positive regulation of cell growth IMP 17545563
genes like me logo Genes that share ontologies with EXOSC4: view

No data available for SIGNOR curated interactions for EXOSC4 Gene

Transcripts for EXOSC4 Gene

Unigene Clusters for EXOSC4 Gene

Exosome component 4:
Representative Sequences:

Inhibitory RNA Products

Clone Products

Flow Cytometry Products

Alternative Splicing Database (ASD) splice patterns (SP) for EXOSC4 Gene

No ASD Table

Relevant External Links for EXOSC4 Gene

GeneLoc Exon Structure for
EXOSC4
ECgene alternative splicing isoforms for
EXOSC4

Expression for EXOSC4 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for EXOSC4 Gene

mRNA differential expression in normal tissues according to GTEx for EXOSC4 Gene

This gene is overexpressed in Whole Blood (x6.3) and Testis (x4.4).

Protein differential expression in normal tissues from HIPED for EXOSC4 Gene

This gene is overexpressed in Breast (15.0) and Peripheral blood mononuclear cells (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EXOSC4 Gene



Protein tissue co-expression partners for EXOSC4 Gene

NURSA nuclear receptor signaling pathways regulating expression of EXOSC4 Gene:

EXOSC4

SOURCE GeneReport for Unigene cluster for EXOSC4 Gene:

Hs.632041
genes like me logo Genes that share expression patterns with EXOSC4: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for EXOSC4 Gene

Orthologs for EXOSC4 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EXOSC4 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EXOSC4 34 35
  • 99.18 (n)
oppossum
(Monodelphis domestica)
Mammalia EXOSC4 35
  • 95 (a)
OneToOne
dog
(Canis familiaris)
Mammalia EXOSC4 34 35
  • 90.61 (n)
cow
(Bos Taurus)
Mammalia EXOSC4 34 35
  • 89.25 (n)
rat
(Rattus norvegicus)
Mammalia Exosc4 34
  • 87.76 (n)
mouse
(Mus musculus)
Mammalia Exosc4 34 16 35
  • 87.48 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia EXOSC4 35
  • 85 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EXOSC4 35
  • 73 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia exosc4 34
  • 76.05 (n)
Str.1967 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.8074 34
zebrafish
(Danio rerio)
Actinopterygii exosc4 34 35
  • 68.57 (n)
zgc73175 34
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13369 34
fruit fly
(Drosophila melanogaster)
Insecta Ski6 34 35
  • 58.3 (n)
worm
(Caenorhabditis elegans)
Secernentea exos-4.1 34 35
  • 49.17 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D09625g 34
  • 45.78 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR035W 34
  • 45.49 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SKI6 34 35
  • 43.78 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons RRP41 34
  • 51.57 (n)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2967 35
  • 53 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU00812 34
  • 52.78 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rrp41 34
  • 48.31 (n)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4725 34
Species where no ortholog for EXOSC4 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • chicken (Gallus gallus)
  • 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)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • 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 EXOSC4 Gene

ENSEMBL:
Gene Tree for EXOSC4 (if available)
TreeFam:
Gene Tree for EXOSC4 (if available)

Paralogs for EXOSC4 Gene

Paralogs for EXOSC4 Gene

genes like me logo Genes that share paralogs with EXOSC4: view

Variants for EXOSC4 Gene

Sequence variations from dbSNP and Humsavar for EXOSC4 Gene

SNP ID Clin Chr 08 pos Sequence Context AA Info Type
rs10113441 -- 144,064,032(+) CCCTC(A/G)CCTCA upstream-variant-2KB
rs111399413 -- 144,070,523(+) ATCTC(-/A)AAAAA intron-variant
rs111633196 -- 144,079,996(+) TGTCA(A/G)TATAG downstream-variant-500B, reference, synonymous-codon, utr-variant-5-prime
rs111730666 -- 144,071,223(+) TCCCC(C/T)CCCCC intron-variant
rs111738325 -- 144,063,774(+) GGAAC(A/C)CGGAG nc-transcript-variant, upstream-variant-2KB, reference, missense

Structural Variations from Database of Genomic Variants (DGV) for EXOSC4 Gene

Variant ID Type Subtype PubMed ID
nsv950015 CNV deletion 24416366
nsv6447 CNV insertion 18451855
nsv612915 CNV loss 21841781
nsv612914 CNV loss 21841781
nsv612907 CNV gain+loss 21841781
nsv612906 CNV loss 21841781
nsv515809 CNV gain+loss 19592680
nsv470250 CNV gain 18288195
nsv470249 CNV loss 18288195
nsv466014 CNV loss 19166990
nsv428208 CNV gain 18775914
nsv1161815 CNV deletion 26073780
nsv1025071 CNV gain 25217958
esv29971 CNV loss 17803354
esv2759651 CNV gain 17122850
dgv906n27 CNV loss 19166990
dgv12433n54 CNV gain 21841781
dgv12431n54 CNV loss 21841781

Variation tolerance for EXOSC4 Gene

Residual Variation Intolerance Score: 55.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.07; 21.89% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EXOSC4 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EXOSC4

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXOSC4 Gene

Disorders for EXOSC4 Gene

Relevant External Links for EXOSC4

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EXOSC4

No disorders were found for EXOSC4 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for EXOSC4 Gene

Publications for EXOSC4 Gene

  1. Three novel components of the human exosome. (PMID: 11110791) Brouwer R. … Pruijn G.J.M. (J. Biol. Chem. 2001) 2 3 4 64
  2. The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates. (PMID: 21255825) Basu U. … Alt F.W. (Cell 2011) 3 4 64
  3. DDX60, a DEXD/H box helicase, is a novel antiviral factor promoting RIG-I-like receptor-mediated signaling. (PMID: 21791617) Miyashita M. … Seya T. (Mol. Cell. Biol. 2011) 3 4 64
  4. Addition of poly(A) and poly(A)-rich tails during RNA degradation in the cytoplasm of human cells. (PMID: 20368444) Slomovic S. … Schuster G. (Proc. Natl. Acad. Sci. U.S.A. 2010) 3 4 64
  5. Dis3-like 1: a novel exoribonuclease associated with the human exosome. (PMID: 20531389) Staals R.H. … Pruijn G.J. (EMBO J. 2010) 3 4 64

Products for EXOSC4 Gene

Sources for EXOSC4 Gene

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