Human Gene EXOSC9 (ENST00000243498.9) Description and Page Index
  Description: Homo sapiens exosome component 9 (EXOSC9), transcript variant 2, mRNA. (from RefSeq NM_005033)
RefSeq Summary (NM_005033): 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].
Gencode Transcript: ENST00000243498.9
Gencode Gene: ENSG00000123737.12
Transcript (Including UTRs)
   Position: hg38 chr4:121,801,317-121,816,909 Size: 15,593 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg38 chr4:121,801,425-121,816,856 Size: 15,432 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr4:121,801,317-121,816,909)mRNA (may differ from genome)Protein (439 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC
ReactomeStanford SOURCEUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Exosome complex component RRP45; AltName: Full=Autoantigen PM/Scl 1; AltName: Full=Exosome component 9; AltName: Full=P75 polymyositis-scleroderma overlap syndrome-associated autoantigen; AltName: Full=Polymyositis/scleroderma autoantigen 1; AltName: Full=Polymyositis/scleroderma autoantigen 75 kDa; Short=PM/Scl-75;
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.
SUBUNIT: 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.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus.
SUBCELLULAR LOCATION: Isoform 1: Nucleus, nucleolus.
SUBCELLULAR LOCATION: Isoform 2: Nucleus, nucleolus.
SUBCELLULAR LOCATION: Isoform 3: Nucleus. Note=Excluded from the nucleolus.
SIMILARITY: Belongs to the RNase PH family.
CAUTION: The six exosome core subunits containing a RNase PH- domain are not phosphorolytically active.

-  MalaCards Disease Associations
  MalaCards Gene Search: EXOSC9
Diseases sorted by gene-association score: polymyositis (16), osteogenesis imperfecta, type xii (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 30.07 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 401.81 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -37.60108-0.348 Picture PostScript Text
3' UTR -11.0053-0.208 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001247 - ExoRNase_PH_dom1
IPR015847 - ExoRNase_PH_dom2
IPR020568 - Ribosomal_S5_D2-typ_fold

Pfam Domains:
PF01138 - 3' exoribonuclease family, domain 1
PF03725 - 3' exoribonuclease family, domain 2

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q06265
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologGenome BrowserNo orthologGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
MGIRGDEnsemblEnsembl SGD
Protein SequenceProtein Sequence Protein Sequence Protein Sequence
AlignmentAlignment Alignment Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000175 3'-5'-exoribonuclease activity
GO:0001102 RNA polymerase II activating transcription factor binding
GO:0003723 RNA binding
GO:0005515 protein binding
GO:0017091 AU-rich element binding
GO:0004532 exoribonuclease activity

Biological Process:
GO:0000467 exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006364 rRNA processing
GO:0006396 RNA processing
GO:0006955 immune response
GO:0030307 positive regulation of cell growth
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
GO:0034473 U1 snRNA 3'-end processing
GO:0034475 U4 snRNA 3'-end processing
GO:0034476 U5 snRNA 3'-end processing
GO:0043488 regulation of mRNA stability
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0071028 nuclear mRNA surveillance
GO:0071035 nuclear polyadenylation-dependent rRNA catabolic process
GO:0071038 nuclear polyadenylation-dependent tRNA catabolic process
GO:0071042 nuclear polyadenylation-dependent mRNA catabolic process

Cellular Component:
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0000228 nuclear chromosome
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0070062 extracellular exosome

-  Descriptions from all associated GenBank mRNAs
  AK301967 - Homo sapiens cDNA FLJ55260 complete cds, highly similar to Exosome complex exonuclease RRP45 (EC 3.1.13.-).
AJ505989 - Homo sapiens mRNA for polymyositis/scleroderma autoantigen 1 (PMSCL1 gene), splice variant 1.
AJ517294 - Homo sapiens mRNA for polymyositis/scleroderma autoantigen 1 (PMSCL1 gene), splice variant 2.
BX649106 - Homo sapiens mRNA; cDNA DKFZp686L2298 (from clone DKFZp686L2298).
BC142978 - Homo sapiens exosome component 9, mRNA (cDNA clone MGC:167080 IMAGE:8860413), complete cds.
AK307548 - Homo sapiens cDNA, FLJ97496.
BC012371 - Homo sapiens exosome component 9, mRNA (cDNA clone IMAGE:3879930), with apparent retained intron.
BC140038 - Synthetic construct Homo sapiens clone IMAGE:100000916, MGC:167226 exosome component 9 (EXOSC9) mRNA, encodes complete protein.
BC140039 - Synthetic construct Homo sapiens clone IMAGE:100013650, MGC:167227 exosome component 9 (EXOSC9) mRNA, encodes complete protein.
KJ897350 - Synthetic construct Homo sapiens clone ccsbBroadEn_06744 EXOSC9 gene, encodes complete protein.
M58460 - Human 75-kD autoantigen (PM-Sc1) mRNA, complete cds.
U09215 - Human PM-Scl-75 autoantigen (PM-sc1) mRNA, complete cds.
AK310894 - Homo sapiens cDNA, FLJ17936.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03018 - RNA degradation

Reactome (by CSHL, EBI, and GO)

Protein Q06265 (Reactome details) participates in the following event(s):

R-HSA-450422 KSRP recruits RNA degradation activities
R-HSA-450431 ZFP36 (TTP) recruits RNA degradation activities
R-HSA-450488 BRF1 Complex recruits RNA degradation activities
R-HSA-430028 Exosome Complex hydrolyzes mRNA by 3' to 5' exoribonuclease digestion
R-HSA-450604 KSRP (KHSRP) binds and destabilizes mRNA
R-HSA-450513 Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA
R-HSA-450385 Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA
R-HSA-450531 Regulation of mRNA stability by proteins that bind AU-rich elements
R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-429958 mRNA decay by 3' to 5' exoribonuclease
R-HSA-8953854 Metabolism of RNA
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-429914 Deadenylation-dependent mRNA decay
R-HSA-72312 rRNA processing

-  Other Names for This Gene
  Alternate Gene Symbols: EXOS9_HUMAN, NM_005033, PMSCL1, Q06265, Q12883, Q4W5P5, Q86Y41, Q86Y48, uc003iea.1, uc003iea.2, uc003iea.3, uc003iea.4
UCSC ID: uc003iea.4
RefSeq Accession: NM_005033
Protein: Q06265 (aka EXOS9_HUMAN or RR45_HUMAN)
CCDS: CCDS3722.2, CCDS34057.1

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.