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Aliases for EXOSC4 Gene

Aliases for EXOSC4 Gene

  • Exosome Component 4 2 3 4
  • RRP41 3 4 6
  • Ribosomal RNA-Processing Protein 41 3 4
  • Exosome Component Rrp41 2 3
  • 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

Summaries for EXOSC4 Gene

GeneCards Summary for EXOSC4 Gene

EXOSC4 (Exosome Component 4) is a Protein Coding gene. Among its related pathways are Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein and Unfolded Protein Response. 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

Genomic Location for EXOSC4 Gene

Start:
144,078,619 bp from pter
End:
144,080,648 bp from pter
Size:
2,030 bases
Orientation:
Plus strand

Genomic View for EXOSC4 Gene

UCSC Golden Path with GeneCards custom track
Cytogenetic band:
Genomic Location for EXOSC4 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXOSC4 Gene

Regulatory Elements 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
    Secondary Accessions:

    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.

    Three dimensional structures from OCA and Proteopedia for EXOSC4 Gene

neXtProt entry for EXOSC4 Gene

Proteomics data for EXOSC4 Gene at MOPED

Post-translational modifications for EXOSC4 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Other Protein References for EXOSC4 Gene

ENSEMBL proteins:
Reactome Protein details:
REFSEQ proteins:

No data available for DME Specific Peptides for EXOSC4 Gene

Domains for EXOSC4 Gene

Protein Domains for EXOSC4 Gene

UniProtKB/Swiss-Prot:

EXOS4_HUMAN
Family:
  • Belongs to the RNase PH family.:
    • Q9NPD3
genes like me logo Genes that share domains with EXOSC4: view

No data available for Gene Families for EXOSC4 Gene

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: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

No data available for Enzyme Numbers (IUBMB) , Animal Models , miRNA , Transcription Factor Targeting 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
Jensen Localization Image for EXOSC4 Gene COMPARTMENTS Subcellular localization image for EXOSC4 gene
Compartment Confidence
nucleus 5
cytosol 4
peroxisome 2
cytoskeleton 1
extracellular 1

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) IDA 20531389
GO:0005634 nucleus IDA 17545563
GO:0005730 nucleolus NAS 11110791
genes like me logo Genes that share ontologies with EXOSC4: view

Pathways for EXOSC4 Gene

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

Pathways by source for EXOSC4 Gene

1 KEGG pathway for EXOSC4 Gene

Gene Ontology (GO) - Biological Process for EXOSC4 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000288 nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay TAS --
GO:0000460 maturation of 5.8S rRNA IMP 20368444
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 17545563
GO:0006364 rRNA processing NAS 11110791
GO:0010467 gene expression TAS --
genes like me logo Genes that share ontologies with EXOSC4: view

Transcripts for EXOSC4 Gene

mRNA/cDNA for EXOSC4 Gene

Unigene Clusters for EXOSC4 Gene

Exosome component 4:
Representative Sequences:

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 for EXOSC4 Gene

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

This gene is overexpressed in Whole Blood (6.3) and Testis (4.4).

Integrated Proteomics: protein expression from ProteomicsDB, PaxDb, MOPED, and MaxQB for EXOSC4 Gene

SOURCE GeneReport for Unigene cluster for EXOSC4 Gene Hs.632041

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

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 36
  • 99.18 (n)
  • 100 (a)
EXOSC4 37
  • 100 (a)
OneToOne
cow
(Bos Taurus)
Mammalia EXOSC4 36
  • 89.25 (n)
  • 97.14 (a)
EXOSC4 37
  • 98 (a)
OneToOne
dog
(Canis familiaris)
Mammalia EXOSC4 36
  • 90.61 (n)
  • 97.96 (a)
EXOSC4 37
  • 98 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Exosc4 36
  • 87.48 (n)
  • 95.92 (a)
Exosc4 16
Exosc4 37
  • 96 (a)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia EXOSC4 37
  • 95 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EXOSC4 37
  • 85 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Exosc4 36
  • 87.76 (n)
  • 97.55 (a)
lizard
(Anolis carolinensis)
Reptilia EXOSC4 37
  • 73 (a)
OneToOne
African clawed frog
(Xenopus laevis)
Amphibia Xl.8074 36
tropical clawed frog
(Silurana tropicalis)
Amphibia exosc4 36
  • 76.05 (n)
  • 81.22 (a)
Str.1967 36
rainbow trout
(Oncorhynchus mykiss)
Actinopterygii Omy.13369 36
zebrafish
(Danio rerio)
Actinopterygii exosc4 36
  • 68.57 (n)
  • 75.1 (a)
exosc4 37
  • 75 (a)
OneToOne
zgc73175 36
fruit fly
(Drosophila melanogaster)
Insecta Ski6 36
  • 58.3 (n)
  • 54.98 (a)
Ski6 37
  • 51 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea exos-4.1 36
  • 49.17 (n)
  • 43.75 (a)
exos-4.1 37
  • 44 (a)
OneToOne
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_ACR035W 36
  • 45.49 (n)
  • 37.34 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SKI6 36
  • 43.78 (n)
  • 36.48 (a)
SKI6 37
  • 34 (a)
OneToMany
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0D09625g 36
  • 45.78 (n)
  • 36.48 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons RRP41 36
  • 51.57 (n)
  • 48.29 (a)
bread mold
(Neurospora crassa)
Ascomycetes NCU00812 36
  • 52.78 (n)
  • 46.08 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes rrp41 36
  • 48.31 (n)
  • 43.22 (a)
sea squirt
(Ciona intestinalis)
Ascidiacea Cin.4725 36
sea squirt
(Ciona savignyi)
Ascidiacea CSA.2967 37
  • 53 (a)
OneToOne
Species with no ortholog for EXOSC4:
  • 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 MAF
rs1132175 -- 144,080,488(+) AGGAC(C/G)ACCTG reference, missense
rs1132180 -- 144,080,491(+) ACCAC(A/C)TGGAG missense, reference
rs1132181 -- 144,080,494(+) ACCTG(A/G)AGCGG missense, reference
rs1132182 -- 144,080,497(+) TGGAG(C/G/T)GGGTG reference, missense
rs1140751 -- 144,080,484(+) CACGA(A/G)GACCA synonymous-codon, reference

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

Variant ID Type Subtype PubMed ID
dgv7935n71 CNV Loss 21882294
dgv7940n71 CNV Loss 21882294
nsv891766 CNV Loss 21882294
dgv906n27 CNV Loss 19166990
nsv470249 CNV Loss 18288195
dgv7948n71 CNV Loss 21882294
dgv7949n71 CNV Loss 21882294
dgv7950n71 CNV Loss 21882294
nsv515809 CNV Gain+Loss 19592680
nsv470250 CNV Gain 18288195
dgv7954n71 CNV Loss 21882294
nsv466014 CNV Loss 19166990
dgv7955n71 CNV Loss 21882294
nsv891807 CNV Loss 21882294
nsv428208 CNV Gain 18775914
nsv891809 CNV Loss 21882294
nsv6447 CNV Insertion 18451855
esv29971 CNV Loss 17803354
dgv2263e1 CNV Complex 17122850

Relevant External Links for EXOSC4 Gene

HapMap Linkage Disequilibrium report
EXOSC4

Disorders for EXOSC4 Gene

No disorders were found for EXOSC4 Gene.

No data available for UniProtKB/Swiss-Prot 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
  2. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. (PMID: 11719186) Chen C.-Y. … Karin M. (Cell 2001) 3 4
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4
  4. Sequence-specific RNA binding mediated by the RNase PH domain of components of the exosome. (PMID: 16912217) Anderson J.R. … Wilusz J. (RNA 2006) 3 4
  5. Reconstitution, activities, and structure of the eukaryotic RNA exosome. (PMID: 17174896) Liu Q. … Lima C.D. (Cell 2006) 3 4

Products for EXOSC4 Gene

Sources for EXOSC4 Gene

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