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Aliases for EXOSC9 Gene

Aliases for EXOSC9 Gene

  • Exosome Component 9 2 3 4 5
  • Polymyositis/Scleroderma Autoantigen 1, 75kDa 2 3
  • Autoantigen PM/Scl 1 3 4
  • PM/Scl-75 3 4
  • PMSCL1 3 4
  • P75 Polymyositis-Scleroderma Overlap Syndrome Associated Autoantigen 3
  • P75 Polymyositis-Scleroderma Overlap Syndrome-Associated Autoantigen 4
  • Polymyositis/Scleroderma Autoantigen 1 (75kD) 2
  • Polymyositis/Scleroderma Autoantigen 75 KDa 4
  • Polymyositis/Scleroderma Autoantigen 1 4
  • Exosome Complex Exonuclease RRP45 3
  • Exosome Complex Component RRP45 3
  • PMSCL Autoantigen, 75kD 3
  • EC 3.1.13 58
  • Rrp45p 3
  • RRP45 3
  • P5 3
  • P6 3

External Ids for EXOSC9 Gene

Previous HGNC Symbols for EXOSC9 Gene

  • PMSCL1

Previous GeneCards Identifiers for EXOSC9 Gene

  • GC04P123182
  • GC04P123080
  • GC04P122941
  • GC04P122722
  • GC04P118449

Summaries for EXOSC9 Gene

Entrez Gene Summary for EXOSC9 Gene

  • This gene encodes a component of the human exosome, a exoribonuclease complex which processes and degrades RNA in the nucleus and cytoplasm. This component may play a role in mRNA degradation and the polymyositis/scleroderma autoantigen complex. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]

GeneCards Summary for EXOSC9 Gene

EXOSC9 (Exosome Component 9) is a Protein Coding gene. Diseases associated with EXOSC9 include Polymyositis and Osteogenesis Imperfecta, Type Xii. Among its related pathways are CDK-mediated phosphorylation and removal of Cdc6 and Pyrimidine metabolism (KEGG). GO annotations related to this gene include poly(A) RNA binding and 3-5-exoribonuclease activity. An important paralog of this gene is EXOSC7.

UniProtKB/Swiss-Prot for EXOSC9 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. EXOSC9 binds to ARE-containing RNAs.

Gene Wiki entry for EXOSC9 Gene

Additional gene information for EXOSC9 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for EXOSC9 Gene

Genomics for EXOSC9 Gene

Regulatory Elements for EXOSC9 Gene

Enhancers for EXOSC9 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
GH04H121821 1.1 ENCODE 49.6 +21.9 21875 3 PKNOX1 ARID4B SIN3A DMAP1 ZNF2 YY1 FOS SP3 CEBPZ SP5 EXOSC9 BBS7 KIAA1109 CCNA2
GH04H122731 1 ENCODE 27.4 +931.9 931908 2 HDGF PKNOX1 ATF1 ARNT ARID4B SIN3A FEZF1 YY1 GLIS2 GATA2 EXOSC9 SPATA5 CETN4P KIAA1109 BBS7 ENSG00000273007 TRPC3 LOC727709
GH04H122763 1.9 FANTOM5 Ensembl ENCODE dbSUPER 11 +963.5 963511 4 PKNOX1 FOXA2 ARNT DMAP1 TCF12 GTF3C2 FOS ATF7 RUNX3 JUNB SPATA5 CETN4P FGF2 ENSG00000237868 BBS12 EXOSC9 NUDT6 CCNA2 LOC727709 RPL34P12
GH04H121070 0.9 ENCODE 18.2 -728.5 -728484 5 ZSCAN4 ZNF2 GLIS2 ZNF366 EGR2 ZNF202 SP3 REST ZNF398 ZNF843 NDNF EXOSC9 LOC105377400
GH04H122699 1.2 Ensembl ENCODE 12.5 +899.0 898999 1 HDAC1 HDGF PKNOX1 ATF1 NFRKB ZBTB40 ZNF766 CBX5 GATA2 EGR1 SPATA5 EXOSC9 ENSG00000237868 FGF2 IL21-AS1 CETN4P BBS12 IL21
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around EXOSC9 on UCSC Golden Path with GeneCards custom track

Promoters for EXOSC9 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000172667 205 1401 MLX ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 ZNF207 SP3

Genomic Location for EXOSC9 Gene

Chromosome:
4
Start:
121,801,295 bp from pter
End:
121,817,021 bp from pter
Size:
15,727 bases
Orientation:
Plus strand

Genomic View for EXOSC9 Gene

Genes around EXOSC9 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
EXOSC9 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for EXOSC9 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for EXOSC9 Gene

Proteins for EXOSC9 Gene

  • Protein details for EXOSC9 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q06265-EXOS9_HUMAN
    Recommended name:
    Exosome complex component RRP45
    Protein Accession:
    Q06265
    Secondary Accessions:
    • Q12883
    • Q4W5P5
    • Q86Y41
    • Q86Y48

    Protein attributes for EXOSC9 Gene

    Size:
    439 amino acids
    Molecular mass:
    48949 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 (PubMed:11719186, PubMed:12788944, PubMed:20531389). Interacts (via C-terminus region) with SETX (via N-terminus domain); the interaction enhances SETX sumoylation (PubMed:24105744).

    Three dimensional structures from OCA and Proteopedia for EXOSC9 Gene

    Alternative splice isoforms for EXOSC9 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for EXOSC9 Gene

Selected DME Specific Peptides for EXOSC9 Gene

Q06265:
  • PVLWTPGTAQIG
  • EERDPVPLSIHHMPICVSFAFFQQGTYLLVDP

Post-translational modifications for EXOSC9 Gene

  • Ubiquitination at isoforms=252, isoforms=267, posLast=101101, and isoforms=2, 3, 4244
  • Modification sites at PhosphoSitePlus

Antibody Products

Domains & Families for EXOSC9 Gene

Gene Families for EXOSC9 Gene

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

Suggested Antigen Peptide Sequences for EXOSC9 Gene

Graphical View of Domain Structure for InterPro Entry

Q06265

UniProtKB/Swiss-Prot:

EXOS9_HUMAN :
  • Belongs to the RNase PH family.
Family:
  • Belongs to the RNase PH family.
genes like me logo Genes that share domains with EXOSC9: view

Function for EXOSC9 Gene

Molecular function for EXOSC9 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. EXOSC9 binds to ARE-containing RNAs.

Enzyme Numbers (IUBMB) for EXOSC9 Gene

Phenotypes From GWAS Catalog for EXOSC9 Gene

Gene Ontology (GO) - Molecular Function for EXOSC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000175 3-5-exoribonuclease activity NAS 11879549
GO:0001102 RNA polymerase II activating transcription factor binding IEA --
GO:0003723 RNA binding NAS 11879549
GO:0004532 NOT exoribonuclease activity IDA 17174896
GO:0005515 protein binding IPI 11719186
genes like me logo Genes that share ontologies with EXOSC9: view
genes like me logo Genes that share phenotypes with EXOSC9: view

Animal Models for EXOSC9 Gene

MGI Knock Outs for EXOSC9:

Animal Model Products

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for EXOSC9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

No data available for Human Phenotype Ontology , miRNA , Transcription Factor Targets and HOMER Transcription for EXOSC9 Gene

Localization for EXOSC9 Gene

Subcellular locations from UniProtKB/Swiss-Prot for EXOSC9 Gene

Cytoplasm. Nucleus. Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Colocalizes with SETX in nuclear foci upon induction of transcription-related DNA damage at the S phase (PubMed:24105744). {ECO:0000269 PubMed:24105744}.
Isoform 1: Nucleus, nucleolus.
Isoform 2: Nucleus, nucleolus.
Isoform 3: Nucleus. Note=Excluded from the nucleolus.

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 EXOSC9 gene
Compartment Confidence
extracellular 5
nucleus 5
cytosol 5
plasma membrane 2
cytoskeleton 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Nucleoli (4)
  • Nucleus (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for EXOSC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000176 nuclear exosome (RNase complex) NAS 11879549
GO:0000177 cytoplasmic exosome (RNase complex) IBA --
GO:0000178 exosome (RNase complex) IEA,IDA 20531389
GO:0000228 nuclear chromosome IDA 24105744
GO:0005634 nucleus IDA,TAS 17545563
genes like me logo Genes that share ontologies with EXOSC9: view

Pathways & Interactions for EXOSC9 Gene

genes like me logo Genes that share pathways with EXOSC9: view

Pathways by source for EXOSC9 Gene

SIGNOR curated interactions for EXOSC9 Gene

Is activated by:

Gene Ontology (GO) - Biological Process for EXOSC9 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000467 exonucleolytic trimming to generate mature 3-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA --
GO:0000956 nuclear-transcribed mRNA catabolic process IMP 17545563
GO:0006364 rRNA processing TAS --
GO:0006396 RNA processing IEA --
GO:0006955 immune response NAS 11879549
genes like me logo Genes that share ontologies with EXOSC9: view

Drugs & Compounds for EXOSC9 Gene

No Compound Related Data Available

Transcripts for EXOSC9 Gene

Unigene Clusters for EXOSC9 Gene

Exosome component 9:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Clone Products

  • Applied Biological Materials Clones for EXOSC9
  • Vectors and viruses for ORF, Lenti, Retro, Adenovirus, AAV, and more

Alternative Splicing Database (ASD) splice patterns (SP) for EXOSC9 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8a · 8b ^ 9 ^ 10a · 10b ^ 11a · 11b · 11c · 11d ^ 12 ^ 13a · 13b ^ 14
SP1: - - - - -
SP2: - - - - - -
SP3: - - - - -
SP4: - - - -
SP5: - - - -
SP6: - - - - - - -
SP7: - - - -
SP8:

Relevant External Links for EXOSC9 Gene

GeneLoc Exon Structure for
EXOSC9
ECgene alternative splicing isoforms for
EXOSC9

Expression for EXOSC9 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for EXOSC9 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for EXOSC9 Gene

This gene is overexpressed in Lung (32.8) and Breast (16.5).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for EXOSC9 Gene



Protein tissue co-expression partners for EXOSC9 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of EXOSC9 Gene:

EXOSC9

SOURCE GeneReport for Unigene cluster for EXOSC9 Gene:

Hs.91728

Evidence on tissue expression from TISSUES for EXOSC9 Gene

  • Liver(4.2)
  • Nervous system(2.1)
genes like me logo Genes that share expression patterns with EXOSC9: view

Primer Products

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for EXOSC9 Gene

Orthologs for EXOSC9 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for EXOSC9 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia EXOSC9 33
  • 99.63 (n)
cow
(Bos Taurus)
Mammalia EXOSC9 34 33
  • 92.26 (n)
OneToOne
dog
(Canis familiaris)
Mammalia EXOSC9 34 33
  • 91.8 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Exosc9 33
  • 88.69 (n)
mouse
(Mus musculus)
Mammalia Exosc9 33 16 34
  • 88.07 (n)
oppossum
(Monodelphis domestica)
Mammalia EXOSC9 34
  • 87 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia EXOSC9 34
  • 82 (a)
OneToOne
chicken
(Gallus gallus)
Aves EXOSC9 34 33
  • 75.43 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia EXOSC9 34
  • 77 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia exosc9 33
  • 71.7 (n)
Str.10876 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.16470 33
zebrafish
(Danio rerio)
Actinopterygii exosc9 34 33
  • 69.16 (n)
OneToOne
Dr.18150 33
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP002348 33
  • 49.28 (n)
fruit fly
(Drosophila melanogaster)
Insecta Rrp45 34
  • 26 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea exos-9 33 34
  • 48.51 (n)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes RRP45 33 34 36
  • 48.86 (n)
K. lactis yeast
(Kluyveromyces lactis)
Saccharomycetes KLLA0C11099g 33
  • 48.38 (n)
A. gosspyii yeast
(Ashbya gossypii)
Saccharomycetes AGOS_AAL124W 33
  • 47.11 (n)
thale cress
(Arabidopsis thaliana)
eudicotyledons CER7 33
  • 51.19 (n)
rice
(Oryza sativa)
Liliopsida Os02g0550700 33
  • 52.89 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes SPCC757.08 33
  • 52.04 (n)
bread mold
(Neurospora crassa)
Ascomycetes NCU00334 33
  • 49.7 (n)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 36 (a)
OneToOne
Species where no ortholog for EXOSC9 was found in the sources mined by GeneCards:
  • 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 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 EXOSC9 Gene

ENSEMBL:
Gene Tree for EXOSC9 (if available)
TreeFam:
Gene Tree for EXOSC9 (if available)

Paralogs for EXOSC9 Gene

Paralogs for EXOSC9 Gene

(2) SIMAP similar genes for EXOSC9 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with EXOSC9: view

Variants for EXOSC9 Gene

Sequence variations from dbSNP and Humsavar for EXOSC9 Gene

SNP ID Clin Chr 04 pos Sequence Context AA Info Type
rs1000264777 -- 121,810,728(+) GCTTG(G/T)TGGTG intron-variant
rs1000941411 -- 121,816,724(+) TAATC(C/G/T)AAAAC intron-variant, utr-variant-3-prime
rs1001019712 -- 121,807,808(+) ACTCT(-/TA)TATAC intron-variant
rs1001152882 -- 121,810,402(+) TGGCC(A/G)GGCAT intron-variant
rs1001262839 -- 121,809,779(+) ACTTA(A/G)CATTC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for EXOSC9 Gene

Variant ID Type Subtype PubMed ID
esv3602016 CNV gain 21293372
nsv997539 CNV gain 25217958

Variation tolerance for EXOSC9 Gene

Residual Variation Intolerance Score: 55.4% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 7.01; 80.09% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for EXOSC9 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
EXOSC9

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for EXOSC9 Gene

Disorders for EXOSC9 Gene

MalaCards: The human disease database

(2) MalaCards diseases for EXOSC9 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
polymyositis
  • pm
osteogenesis imperfecta, type xii
  • osteogenesis imperfecta type 12
- elite association - COSMIC cancer census association via MalaCards

Relevant External Links for EXOSC9

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
EXOSC9
genes like me logo Genes that share disorders with EXOSC9: view

No data available for UniProtKB/Swiss-Prot and Genatlas for EXOSC9 Gene

Publications for EXOSC9 Gene

  1. A SUMO-dependent interaction between Senataxin and the exosome, disrupted in the neurodegenerative disease AOA2, targets the exosome to sites of transcription-induced DNA damage. (PMID: 24105744) Richard P … Manley JL (Genes & development 2013) 3 4 60
  2. Dis3-like 1: a novel exoribonuclease associated with the human exosome. (PMID: 20531389) Staals RH … Pruijn GJ (The EMBO journal 2010) 3 4 60
  3. Human cell growth requires a functional cytoplasmic exosome, which is involved in various mRNA decay pathways. (PMID: 17545563) van Dijk EL … Pruijn GJ (RNA (New York, N.Y.) 2007) 3 4 60
  4. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 60
  5. Reconstitution, activities, and structure of the eukaryotic RNA exosome. (PMID: 17174896) Liu Q … Lima CD (Cell 2006) 3 4 60

Products for EXOSC9 Gene

Sources for EXOSC9 Gene

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