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EXOSC9 exosome component 9 [ Homo sapiens (human) ]

Gene ID: 5393, updated on 11-Sep-2019

Summary

Official Symbol
EXOSC9provided by HGNC
Official Full Name
exosome component 9provided by HGNC
Primary source
HGNC:HGNC:9137
See related
Ensembl:ENSG00000123737 MIM:606180
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
p5; p6; PCH1D; RRP45; PMSCL1; Rrp45p; PM/Scl-75
Summary
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]
Expression
Broad expression in testis (RPKM 24.9), bone marrow (RPKM 19.1) and 24 other tissues See more
Orthologs

Genomic context

See EXOSC9 in Genome Data Viewer
Location:
4q27
Exon count:
14
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 4 NC_000004.12 (121801323..121817021)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 4 NC_000004.11 (122722445..122738176)

Chromosome 4 - NC_000004.12Genomic Context describing neighboring genes Neighboring gene annexin A5 Neighboring gene transmembrane protein 155 Neighboring gene uncharacterized LOC100192379 Neighboring gene cyclin A2 Neighboring gene Bardet-Biedl syndrome 7 Neighboring gene transient receptor potential cation channel subfamily C member 3 Neighboring gene uncharacterized LOC102724158

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • ATF4 activates genes, organism-specific biosystem (from REACTOME)
    ATF4 activates genes, organism-specific biosystemATF4 is a transcription factor and activates expression of IL-8, MCP1, IGFBP-1, CHOP, HERP1 and ATF3.
  • Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA, organism-specific biosystemButyrate Response Factor 1 (BRF1, ZFP36L1, not to be confused with transcription factor IIIB) binds AU-rich elements in the 3' region of mRNAs. After binding, BRF1 recruits exonucleases (XRN1 and the...
  • Deadenylation-dependent mRNA decay, organism-specific biosystem (from REACTOME)
    Deadenylation-dependent mRNA decay, organism-specific biosystemAfter undergoing rounds of translation, mRNA is normally destroyed by the deadenylation-dependent pathway. Though the trigger is unclear, deadenylation likely proceeds in two steps: one catalyzed by...
  • Exosome, eukaryotes, organism-specific biosystem (from KEGG)
    Exosome, eukaryotes, organism-specific biosystemStructural complex; Genetic information processing; RNA processing
  • Exosome, eukaryotes, conserved biosystem (from KEGG)
    Exosome, eukaryotes, conserved biosystemStructural complex; Genetic information processing; RNA processing
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    KSRP (KHSRP) binds and destabilizes mRNA, organism-specific biosystemKSRP binds to AU-rich sequences in the 3' untranslated regions of mRNAs. KSRP causes the bound mRNA to be targeted for hydrolysis by recruiting exonucleases and decapping enzymes. The activity of KSR...
  • Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystem (from REACTOME)
    Major pathway of rRNA processing in the nucleolus and cytosol, organism-specific biosystemIn humans, a 47S precursor rRNA (pre-rRNA) is transcribed by RNA polymerase I from rRNA-encoding genes (rDNA) at the boundary of the fibrillar center and the dense fibrillar components of the nucleol...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • PERK regulates gene expression, organism-specific biosystem (from REACTOME)
    PERK regulates gene expression, organism-specific biosystemPERK (EIF2AK3) is a single-pass transmembrane protein located in the endoplasmic reticulum (ER) membrane such that the N-terminus of PERK is luminal and the C-terminus is cytosolic. PERK is maintaine...
  • RNA degradation, organism-specific biosystem (from KEGG)
    RNA degradation, organism-specific biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • RNA degradation, conserved biosystem (from KEGG)
    RNA degradation, conserved biosystemThe correct processing, quality control and turnover of cellular RNA molecules are critical to many aspects in the expression of genetic information. In eukaryotes, two major pathways of mRNA decay e...
  • Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystem (from REACTOME)
    Regulation of mRNA stability by proteins that bind AU-rich elements, organism-specific biosystemRNA elements rich in adenine and uracil residues (AU-rich elements) bind specific proteins which either target the RNA for degradation or, more rarely, stabilize the RNA. The activity of the AU-eleme...
  • Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystem (from REACTOME)
    Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA, organism-specific biosystemTristetraproline (TTP) binds RNAs that contain AU-rich elements and recruits enzymes that degrade RNA. TTP interacts with the exosome (3' to 5' exonuclease), XRN1 (5' to 3' exonuclease), and the deca...
  • Unfolded Protein Response (UPR), organism-specific biosystem (from REACTOME)
    Unfolded Protein Response (UPR), organism-specific biosystemThe Unfolded Protein Response (UPR) is a regulatory system that protects the Endoplasmic Reticulum (ER) from overload. The UPR is provoked by the accumulation of improperly folded protein in the ER d...
  • mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystem (from REACTOME)
    mRNA decay by 3' to 5' exoribonuclease, organism-specific biosystemThe degradation of mRNA from 3' to 5' occurs in two steps. First, the exosome exoribonuclease complex binds the 3' end of the oligoadenylated mRNA and hydrolyzes it from 3' to 5', yielding ribonucleo...
  • rRNA processing, organism-specific biosystem (from REACTOME)
    rRNA processing, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...
  • rRNA processing in the nucleus and cytosol, organism-specific biosystem (from REACTOME)
    rRNA processing in the nucleus and cytosol, organism-specific biosystemEach eukaryotic cytosolic ribosome contains 4 molecules of RNA: 28S rRNA (25S rRNA in yeast), 5.8S rRNA, and 5S rRNA in the 60S subunit and 18S rRNA in the 40S subunit. The 18S rRNA, 5.8S rRNA, and 2...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5'-exoribonuclease activity NAS
Non-traceable Author Statement
more info
PubMed 
AU-rich element binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding HDA PubMed 
RNA binding NAS
Non-traceable Author Statement
more info
PubMed 
RNA polymerase II activating transcription factor binding IEA
Inferred from Electronic Annotation
more info
 
NOT exoribonuclease activity IDA
Inferred from Direct Assay
more info
PubMed 
mRNA 3'-UTR AU-rich region binding IDA
Inferred from Direct Assay
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
U1 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U4 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
U5 snRNA 3'-end processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay IMP
Inferred from Mutant Phenotype
more info
PubMed 
exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay TAS
Traceable Author Statement
more info
 
exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
immune response NAS
Non-traceable Author Statement
more info
PubMed 
nuclear mRNA surveillance IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear mRNA surveillance IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear polyadenylation-dependent mRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear polyadenylation-dependent rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear polyadenylation-dependent rRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear polyadenylation-dependent tRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear-transcribed mRNA catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of cell growth IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
rRNA catabolic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
rRNA processing NAS
Non-traceable Author Statement
more info
PubMed 
rRNA processing TAS
Traceable Author Statement
more info
 
regulation of mRNA stability TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
extracellular exosome HDA PubMed 
nuclear chromosome IDA
Inferred from Direct Assay
more info
PubMed 
nuclear exosome (RNase complex) IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nuclear exosome (RNase complex) IDA
Inferred from Direct Assay
more info
PubMed 
nuclear exosome (RNase complex) NAS
Non-traceable Author Statement
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
exosome complex component RRP45
Names
P75 polymyositis-scleroderma overlap syndrome associated autoantigen
PMSCL autoantigen, 75kD
autoantigen PM/Scl 1
exosome complex exonuclease RRP45
polymyositis/scleroderma autoantigen 1, 75kDa
NP_001029366.1
NP_005024.2
XP_011530337.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_029848.1 RefSeqGene

    Range
    5007..20705
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001034194.2NP_001029366.1  exosome complex component RRP45 isoform 1

    See identical proteins and their annotated locations for NP_001029366.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AJ517294, BU615347
    Consensus CDS
    CCDS34057.1
    UniProtKB/Swiss-Prot
    Q06265
    Related
    ENSP00000368984.3, ENST00000379663.7
    Conserved Domains (2) summary
    cd11368
    Location:6264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]
  2. NM_005033.3NP_005024.2  exosome complex component RRP45 isoform 2

    See identical proteins and their annotated locations for NP_005024.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an in-frame exon in the 3' coding region, compared to variant 1. This results in a shorter protein (isoform 2), compared to isoform 1.
    Source sequence(s)
    AC079341
    Consensus CDS
    CCDS3722.2
    UniProtKB/Swiss-Prot
    Q06265
    Related
    ENSP00000243498.5, ENST00000243498.9
    Conserved Domains (2) summary
    cd11368
    Location:6264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000004.12 Reference GRCh38.p13 Primary Assembly

    Range
    121801323..121817021
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011532035.3XP_011530337.1  exosome complex component RRP45 isoform X1

    See identical proteins and their annotated locations for XP_011530337.1

    UniProtKB/TrEMBL
    B4DXG8
    Conserved Domains (2) summary
    cd11368
    Location:6264
    RNase_PH_RRP45; RRP45 subunit of eukaryotic exosome
    COG2123
    Location:10271
    Rrp42; Exosome complex RNA-binding protein Rrp42, RNase PH superfamily [Translation, ribosomal structure and biogenesis]

RNA

  1. XR_001741241.2 RNA Sequence

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