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EXOSC1 Gene(Protein Coding)

Exosome Component 1

GCID:
GC10M097435
GIFtS:
46
Genes Participants
UDN Logo

Aliases for EXOSC1 Gene

Aliases for EXOSC1 Gene

  • Exosome Component 1 2 3 4 5
  • CSL4 3 4
  • Homolog Of Yeast Exosomal Core Protein CSL4 3
  • CSL4 Exosomal Core Protein Homolog (Yeast) 2
  • 3-5 Exoribonuclease CSL4 Homolog 3
  • Exosome Complex Component CSL4 3
  • Exosomal Core Protein CSL4 3
  • CGI-108 3
  • Csl4p 3
  • Ski4p 3
  • SKI4 3
  • P13 3

External Ids for EXOSC1 Gene

Previous GeneCards Identifiers for EXOSC1 Gene

  • GC10M098856
  • GC10M099181
  • GC10M092821
  • GC10M099191
  • GC10M099192
  • GC10M099198
  • GC10M099205

Summaries for EXOSC1 Gene

Entrez Gene Summary for EXOSC1 Gene

  • This gene encodes a core component of the exosome. The mammalian exosome is required for rapid degradation of AU rich element-containing RNAs but not for poly(A) shortening. The association of this protein with the exosome is mediated by protein-protein interactions with ribosomal RNA-processing protein 42 and ribosomal RNA-processing protein 46. Alternative splicing of this gene results in multiple transcript variants. [provided by RefSeq, Jan 2016]

GeneCards Summary for EXOSC1 Gene

EXOSC1 (Exosome Component 1) is a Protein Coding gene. Diseases associated with EXOSC1 include Cerebellopontine Angle Tumor and Charcot-Marie-Tooth Disease, Demyelinating, Type 1C. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Gene Expression. Gene Ontology (GO) annotations related to this gene include RNA binding and exoribonuclease activity.

UniProtKB/Swiss-Prot for EXOSC1 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. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.

Gene Wiki entry for EXOSC1 Gene

Additional gene information for EXOSC1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EXOSC1 Gene

Genomics for EXOSC1 Gene

Products:

  1. Regulatory Element

GeneHancer (GH) Regulatory Elements for EXOSC1 Gene

Promoters and enhancers for EXOSC1 Gene
GeneHancer (GH) Identifier GH Type GH
Score		 GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites		 Gene Targets
GH10I097444 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 550.8 -0.7 -669 3.7 PKNOX1 SMAD1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF2 IRF4 YY1 ZDHHC16 EXOSC1 PGAM1 ENSG00000200737 RRP12 MMS19 UBTD1 ANKRD2
GH10I097331 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 28.5 +112.4 112367 4.9 HDGF CLOCK FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZBTB7B FRAT2 LOC105378448 EXOSC1 RPL13AP5 NPM1P26 R3HCC1L LOXL4 ENSG00000230928 TM9SF3 SLIT1
GH10I097421 Enhancer 1.1 ENCODE dbSUPER 59.4 +22.7 22659 2.8 ZNF493 ZNF529 ZFP64 BATF ZNF213 ZNF354C ZNF138 ZNF366 ETV6 FOS GC10M097425 PIR45391 MMS19 LCOR EXOSC1 R3HCC1L NPM1P26 TM9SF3 RPL13AP5 MARVELD1
GH10I098132 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 24.7 -688.4 -688446 3.2 HDGF PKNOX1 ARID4B SIN3A FEZF1 DMAP1 ZNF2 IRF4 YY1 POLR2B R3HCC1L HPS1 LOXL4 EXOSC1 MMS19 MARVELD1 ENSG00000278752
GH10I096579 Enhancer 1.4 Ensembl ENCODE dbSUPER 28.8 +865.0 865020 2.7 FEZF1 GLI4 ZNF2 ZNF121 ZNF416 KLF7 ZNF548 ATF7 KLF13 ZNF202 ZNF518A TCTN3 MMS19 CCNJ LCOR EXOSC1 NPM1P26 TM9SF3 MIR607 ALDH18A1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around EXOSC1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the EXOSC1 gene promoter:

Genomic Locations for EXOSC1 Gene

Genomic Locations for EXOSC1 Gene
chr10:97,435,909-97,446,017
(GRCh38/hg38)
Size:
10,109 bases
Orientation:
Minus strand
chr10:99,195,666-99,205,774
(GRCh37/hg19)

Genomic View for EXOSC1 Gene

Genes around EXOSC1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXOSC1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXOSC1 Gene
GeneLoc Logo Genomic Neighborhood • Exon Structure • Gene Density

RefSeq DNA sequence for EXOSC1 Gene

Proteins for EXOSC1 Gene

Products:

  1. Antibody
  2. Protein
  3. Assay

  • Protein details for EXOSC1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q9Y3B2-EXOS1_HUMAN
    Recommended name:
    Exosome complex component CSL4
    Protein Accession:
    Q9Y3B2
    Secondary Accessions:
    • B2R9B3
    • Q5JTH3

    Protein attributes for EXOSC1 Gene

    Size:
    195 amino acids
    Molecular mass:
    21452 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 EXOSC5, EXOSC7 and EXOSC10. Interacts with DDX60.

    Three dimensional structures from OCA and Proteopedia for EXOSC1 Gene

neXtProt entry for EXOSC1 Gene

Protein Expression for EXOSC1 Gene

See protein expression from ProteomicsDB, MOPED, PaxDb, and MaxQB

Post-translational modifications for EXOSC1 Gene

  • Ubiquitination at posLast=9696 and Lys120

Other Protein References for EXOSC1 Gene

ENSEMBL proteins:
REFSEQ proteins:

No data available for DME Specific Peptides for EXOSC1 Gene

Domains & Families for EXOSC1 Gene

Gene Families for EXOSC1 Gene

HGNC:
Human Protein Atlas (HPA):
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for EXOSC1 Gene

InterPro:
Blocks:
ProtoNet:

Suggested Antigen Peptide Sequences for EXOSC1 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry

Q9Y3B2

UniProtKB/Swiss-Prot:

EXOS1_HUMAN :
  • Belongs to the CSL4 family.
Family:
  • Belongs to the CSL4 family.
genes like me logo Genes that share domains with EXOSC1: view

Function for EXOSC1 Gene

Products:

  1. Animal Model
  2. CRISPR
  3. miRNA
  4. Inhibitory RNA
  5. Clone
  6. Cell Line

Molecular function for EXOSC1 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. EXOSC1 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC6 and EXOSC8.

Phenotypes From GWAS Catalog for EXOSC1 Gene

Gene Ontology (GO) - Molecular Function for EXOSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003723 RNA binding IEA,NAS 11812149
GO:0004532 NOT exoribonuclease activity IDA 17174896
GO:0005515 protein binding IPI 11812149
genes like me logo Genes that share ontologies with EXOSC1: view
genes like me logo Genes that share phenotypes with EXOSC1: view

Animal Model Products

miRNA for EXOSC1 Gene

miRTarBase miRNAs that target EXOSC1

Clone Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for EXOSC1 Gene

Localization for EXOSC1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXOSC1 Gene

Nucleus, nucleolus. Nucleus. Cytoplasm.

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 EXOSC1 gene
Compartment Confidence
nucleus 5
cytosol 5
extracellular 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nuclear bodies (2)
  • Nucleoplasm (2)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EXOSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 nuclear exosome (RNase complex) IBA --
GO:0000178 exosome (RNase complex) NAS,IEA 11812149
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005730 nucleolus IDA,IEA 11812149
genes like me logo Genes that share ontologies with EXOSC1: view

Pathways & Interactions for EXOSC1 Gene

genes like me logo Genes that share pathways with EXOSC1: view

Pathways by source for EXOSC1 Gene

1 KEGG pathway for EXOSC1 Gene
1 GeneGo (Thomson Reuters) pathway for EXOSC1 Gene

Gene Ontology (GO) - Biological Process for EXOSC1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006364 rRNA processing TAS --
GO:0043488 regulation of mRNA stability TAS --
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS --
genes like me logo Genes that share ontologies with EXOSC1: view

No data available for SIGNOR curated interactions for EXOSC1 Gene

Drugs & Compounds for EXOSC1 Gene

Products:

  1. Drug
No Compound Related Data Available

Transcripts for EXOSC1 Gene

Products:

  1. CRISPR
  2. miRNA
  3. Inhibitory RNA
  4. Clone

mRNA/cDNA for EXOSC1 Gene

(8) REFSEQ mRNAs :
(3) Additional mRNA sequences :
(183) Selected AceView cDNA sequences:
(11) Ensembl transcripts including schematic representations, and UCSC links where relevant :

Unigene Clusters for EXOSC1 Gene

Exosome component 1:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for EXOSC1 Gene

ExUns: 1 ^ 2a · 2b ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7a · 7b ^ 8a · 8b ^ 9a · 9b · 9c
SP1: - - - -
SP2: - - - - -
SP3: -
SP4: - -
SP5: - -
SP6:
SP7: -

Relevant External Links for EXOSC1 Gene

GeneLoc Exon Structure for
EXOSC1
ECgene alternative splicing isoforms for
EXOSC1

Expression for EXOSC1 Gene

Products:

  1. Primer

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EXOSC1 Gene

mRNA expression in normal human tissues for EXOSC1 Gene
mRNA expression by BioGPS for EXOSC1 GenemRNA expression by GTEx for EXOSC1 Gene

Protein differential expression in normal tissues from HIPED for EXOSC1 Gene

This gene is overexpressed in Liver (53.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EXOSC1 Gene



Protein tissue co-expression partners for EXOSC1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EXOSC1 Gene:

EXOSC1

SOURCE GeneReport for Unigene cluster for EXOSC1 Gene:

Hs.632089

Evidence on tissue expression from TISSUES for EXOSC1 Gene

  • Nervous system(4.5)
genes like me logo Genes that share expression patterns with EXOSC1: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EXOSC1 Gene

Orthologs for EXOSC1 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EXOSC1 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
 Mammalia EXOSC1 33 34
  • 99.49 (n)
oppossum
(Monodelphis domestica)
 Mammalia EXOSC1 34
  • 92 (a)
 OneToOne
cow
(Bos Taurus)
 Mammalia EXOSC1 33 34
  • 91.62 (n)
dog
(Canis familiaris)
 Mammalia EXOSC1 33 34
  • 90.94 (n)
platypus
(Ornithorhynchus anatinus)
 Mammalia EXOSC1 34
  • 90 (a)
 OneToOne
mouse
(Mus musculus)
 Mammalia Exosc1 33 16 34
  • 89.74 (n)
rat
(Rattus norvegicus)
 Mammalia Exosc1 33
  • 89.23 (n)
chicken
(Gallus gallus)
 Aves EXOSC1 34
  • 87 (a)
 OneToOne
lizard
(Anolis carolinensis)
 Reptilia EXOSC1 34
  • 84 (a)
 OneToOne
tropical clawed frog
(Silurana tropicalis)
 Amphibia exosc1 33
  • 70.14 (n)
Str.6115 33
zebrafish
(Danio rerio)
 Actinopterygii exosc1 33 34
  • 69.98 (n)
rainbow trout
(Oncorhynchus mykiss)
 Actinopterygii Omy.1793 33
African malaria mosquito
(Anopheles gambiae)
 Insecta AgaP_AGAP008063 33
  • 54.63 (n)
fruit fly
(Drosophila melanogaster)
 Insecta Csl4 33 34
  • 54.03 (n)
worm
(Caenorhabditis elegans)
 Secernentea exos-1 33 34
  • 45.81 (n)
baker's yeast
(Saccharomyces cerevisiae)
 Saccharomycetes CSL4 33 34 36
  • 52.03 (n)
A. gosspyii yeast
(Ashbya gossypii)
 Saccharomycetes AGOS_ABL199W 33
  • 51.45 (n)
K. lactis yeast
(Kluyveromyces lactis)
 Saccharomycetes KLLA0D19701g 33
  • 49.23 (n)
thale cress
(Arabidopsis thaliana)
 eudicotyledons AT5G38890 33
  • 52.62 (n)
rice
(Oryza sativa)
 Liliopsida Os02g0815800 33
  • 55.15 (n)
sea squirt
(Ciona savignyi)
 Ascidiacea -- 34
  • 54 (a)
 OneToOne
bread mold
(Neurospora crassa)
 Ascomycetes NCU04155 33
  • 52.51 (n)
fission yeast
(Schizosaccharomyces pombe)
 Schizosaccharomycetes csl4 33
  • 48.15 (n)
sea squirt
(Ciona intestinalis)
 Ascidiacea Cin.2962 33
Species where no ortholog for EXOSC1 was found in the sources mined by GeneCards:
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • 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)
  • 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 EXOSC1 Gene

ENSEMBL:
Gene Tree for EXOSC1 (if available)
TreeFam:
Gene Tree for EXOSC1 (if available)

Paralogs for EXOSC1 Gene

No data available for Paralogs for EXOSC1 Gene

Variants for EXOSC1 Gene

Sequence variations from dbSNP and Humsavar for EXOSC1 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
rs1000058773 -- 97,446,901(-) T/A upstream_transcript_variant
rs1000433704 -- 97,438,159(-) C/A/T intron_variant
rs1000519724 -- 97,443,213(-) G/A intron_variant
rs1000572108 -- 97,443,546(-) G/A intron_variant
rs1000675822 -- 97,437,415(-) A/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for EXOSC1 Gene

Variant ID Type Subtype PubMed ID
esv3624313 CNV gain 21293372
nsv1110852 OTHER inversion 24896259
nsv467440 CNV loss 19166990
nsv552025 CNV loss 21841781

Variation tolerance for EXOSC1 Gene

Residual Variation Intolerance Score: 42.6% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 0.50; 10.92% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for EXOSC1 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EXOSC1

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXOSC1 Gene

Disorders for EXOSC1 Gene

MalaCards: The human disease database

(2) MalaCards diseases for EXOSC1 Gene - From: DISEASES

Disorder Aliases PubMed IDs
cerebellopontine angle tumor
  • neoplasm of the cerebellopontine angle
charcot-marie-tooth disease, demyelinating, type 1c
  • cmt1c
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for EXOSC1

ATLAS of Genetics and Cytogenetics in Oncology and Haematology
genes like me logo Genes that share disorders with EXOSC1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EXOSC1 Gene

Publications for EXOSC1 Gene

  1. Protein-protein interactions of hCsl4p with other human exosome subunits. (PMID: 11812149) Raijmakers R … Pruijn GJ (Journal of molecular biology 2002) 2 3 4 22 58
  2. AU binding proteins recruit the exosome to degrade ARE-containing mRNAs. (PMID: 11719186) Chen CY … Karin M (Cell 2001) 2 3 4 58
  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 (Molecular and cellular biology 2011) 3 4 58
  4. Dis3-like 1: a novel exoribonuclease associated with the human exosome. (PMID: 20531389) Staals RH … Pruijn GJ (The EMBO journal 2010) 3 4 58
  5. Reconstitution, activities, and structure of the eukaryotic RNA exosome. (PMID: 17174896) Liu Q … Lima CD (Cell 2006) 3 4 58

Products for EXOSC1 Gene

Sources for EXOSC1 Gene

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