EXOSC9

Protein identityUniProt · HPA

UniProt accession

Q06265

Gene

EXOSC9

Ensembl

ENSG00000123737

Chromosome

4

Canonical length

439 aa

Protein class

Disease related genes, Human disease related genes, Predicted intracellular proteins

Subcellular location

Nucleoplasm,Nucleoli

OverviewNCBI 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]

Canonical amino-acid sequenceUniProt

439 residues, UniProt reviewed canonical sequence.

>Q06265|EXOSC9
     1  MKETPLSNCE RRFLLRAIEE KKRLDGRQTY DYRNIRISFG TDYGCCIVEL GKTRVLGQVS
    61  CELVSPKLNR ATEGILFFNL ELSQMAAPAF EPGRQSDLLV KLNRLMERCL RNSKCIDTES
   121  LCVVAGEKVW QIRVDLHLLN HDGNIIDAAS IAAIVALCHF RRPDVSVQGD EVTLYTPEER
   181  DPVPLSIHHM PICVSFAFFQ QGTYLLVDPN EREERVMDGL LVIAMNKHRE ICTIQSSGGI
   241  MLLKDQVLRC SKIAGVKVAE ITELILKALE NDQKVRKEGG KFGFAESIAN QRITAFKMEK
   301  APIDTSDVEE KAEEIIAEAE PPSEVVSTPV LWTPGTAQIG EGVENSWGDL EDSEKEDDEG
   361  GGDQAIILDG IKMDTGVEVS DIGSQDAPII LSDSEEEEMI ILEPDKNPKK IRTQTTSAKQ
   421  EKAPSKKPVK RRKKKRAAN

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against EXOSC9 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability

Intracellular

Secreted

No

Transmembrane segments

0

Mean surface accessibility (rSASA)

0.42

Highest tissue expression

41 nTPM

Expression across tissuesHPA

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about EXOSC9.

Disease | AllUniProt

Conditions EXOSC9 is implicated in, by any mechanism.

• Pontocerebellar hypoplasia 1D (PCH1D) MIM:618065

Disease | GeneticClinVar

32 pathogenic / likely-pathogenic of 343 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

• Pontocerebellar hypoplasia, type 1D
• Cerebral atrophy
• Pontoneocerebellar hypoplasia
• Kabuki syndrome 2
• Thymoma

Disease | AutoantibodyPubMed

Conditions in which antibodies against EXOSC9 are reported. Each links to that disease's full target list.

• Scleroderma, Systemic 3

ReferencesPubMed · IEDB

Publications for EXOSC9 from three distinct lines of evidence, kept separate because they answer different questions: whether antibodies are directed at the protein, whether a B-cell epitope has been mapped on it, and whether a T-cell epitope has. Each is labelled with its source.

Sources: PubMed — antigen-level antibody evidence from a custom retrieval. Records matching a controlled set of autoantibody terms (the MeSH descriptors Autoantibodies and Autoantigens, with title and abstract term variants) were obtained through NCBI E-utilities, and their titles and abstracts parsed for constructions that direct an antibody at a named protein rather than for co-occurrence. Captured names were resolved against UniProt nomenclature and each antigen adjudicated individually against the source text. Bibliographic records from PubMed and MeSH, U.S. National Library of Medicine; citation metrics from NIH iCite (Hutchins et al., PLoS Biology 2016). Titles link to PubMed; abstracts are not reproduced here. The NLM does not endorse this analysis.

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)

1.11

gnomAD pLI

0

gnomAD missense Z

0.15

DepMap mean gene effect

-1.1

DepMap dependency class

common

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

• exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
• immune response
• mRNA catabolic process
• nuclear mRNA surveillance
• nuclear polyadenylation-dependent rRNA catabolic process
• nuclear-transcribed mRNA catabolic process
• positive regulation of cell growth
• positive regulation of transcription by RNA polymerase II
• RNA catabolic process
• RNA processing
• rRNA catabolic process
• rRNA processing
• TRAMP-dependent tRNA surveillance pathway
• U1 snRNA 3'-end processing
• U4 snRNA 3'-end processing
• U5 snRNA 3'-end processing

Molecular functions

• 3'-5'-RNA exonuclease activity
• mRNA 3'-UTR AU-rich region binding
• RNA binding
• RNA polymerase II-specific DNA-binding transcription factor binding

Cellular components

• cytoplasm
• cytoplasmic exosome (RNase complex)
• cytosol
• exosome (RNase complex)
• extracellular exosome
• nuclear chromosome
• nuclear exosome (RNase complex)
• nucleolar exosome (RNase complex)
• nucleolus
• nucleoplasm
• nucleus

Protein domainsUniProt · Pfam · InterPro

• Exoribonuclease, phosphorolytic domain 1
• Exoribonuclease, phosphorolytic domain 2
• Ribosomal protein uS5 domain 2-type superfamily
• PNPase/RNase PH domain superfamily
• Exoribonuclease, PH domain 2 superfamily
• Exosome complex component Rrp42 subfamily
• 3' exoribonuclease family, domain 1
• 3' exoribonuclease family, domain 2
• Exosome complex component RRP45

KeywordsUniProt

• Acetylation
• Cytoplasm
• Exosome
• Isopeptide bond
• Neurodegeneration
• Nucleus
• Phosphoprotein
• RNA-binding
• rRNA processing
• Ubl conjugation

InteractionsUniProt · HPA

Protein binding partners of EXOSC9 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

• DIS3
• EXOSC3
• EXOSC4
• EXOSC5
• SUMO1
• EXOSC1
• EXOSC2
• EXOSC7