Human Gene EXOSC4 (ENST00000316052.6)
  Description: Homo sapiens exosome component 4 (EXOSC4), mRNA. (from RefSeq NM_019037)
Gencode Transcript: ENST00000316052.6
Gencode Gene: ENSG00000178896.9
Transcript (Including UTRs)
   Position: hg38 chr8:144,078,672-144,080,648 Size: 1,977 Total Exon Count: 3 Strand: +
Coding Region
   Position: hg38 chr8:144,078,729-144,080,601 Size: 1,873 Coding Exon Count: 3 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated at UCSC: 2021-01-14 15:32:12

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr8:144,078,672-144,080,648)mRNA (may differ from genome)Protein (245 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsHGNC

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=Exosome complex component RRP41; AltName: Full=Exosome component 4; AltName: Full=Ribosomal RNA-processing protein 41; AltName: Full=p12A;
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. EXOSC4 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. Interacts with DDX60.
INTERACTION: Q9Y3B2:EXOSC1; NbExp=3; IntAct=EBI-371823, EBI-371892; Q13868:EXOSC2; NbExp=4; IntAct=EBI-371823, EBI-301735; Q9NQT5:EXOSC3; NbExp=3; IntAct=EBI-371823, EBI-371866;
SUBCELLULAR LOCATION: Cytoplasm. Nucleus, nucleolus. Nucleus.
SIMILARITY: Belongs to the RNase PH family.
CAUTION: The six exosome core subunits containing a RNase PH- domain are not phosphorolytically active.

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C016403 2,4-dinitrotoluene
  • C023514 2,6-dinitrotoluene
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C009505 4,4'-diaminodiphenylmethane
  • D016604 Aflatoxin B1
  • D001564 Benzo(a)pyrene
  • D002994 Clofibrate
  • D019327 Copper Sulfate
  • D016572 Cyclosporine
          more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 61.33 RPKM in Testis
Total median expression: 453.41 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 -15.8057-0.277 Picture PostScript Text
3' UTR -1.8047-0.038 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 Q9NPD3
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 BrowserGenome BrowserGenome Browser
Gene Details    Gene Details
Gene Sorter    Gene Sorter
Protein SequenceProtein Sequence Protein SequenceProtein SequenceProtein Sequence
AlignmentAlignment AlignmentAlignmentAlignment

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

Biological Process:
GO:0000460 maturation of 5.8S rRNA
GO:0000956 nuclear-transcribed mRNA catabolic process
GO:0006364 rRNA processing
GO:0016075 rRNA catabolic process
GO:0030307 positive regulation of cell growth
GO:0031125 rRNA 3'-end processing
GO:0034427 nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5'
GO:0034475 U4 snRNA 3'-end processing
GO:0043488 regulation of mRNA stability
GO:0043928 exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay
GO:0045006 DNA deamination
GO:0051607 defense response to virus
GO:0071028 nuclear mRNA surveillance
GO:0071044 histone mRNA catabolic process
GO:0071051 polyadenylation-dependent snoRNA 3'-end processing
GO:0090503 RNA phosphodiester bond hydrolysis, exonucleolytic

Cellular Component:
GO:0000176 nuclear exosome (RNase complex)
GO:0000177 cytoplasmic exosome (RNase complex)
GO:0000178 exosome (RNase complex)
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0035327 transcriptionally active chromatin
GO:0045111 intermediate filament cytoskeleton

-  Descriptions from all associated GenBank mRNAs
  AF281133 - Homo sapiens exosome component Rrp41 mRNA, complete cds.
AK000598 - Homo sapiens cDNA FLJ20591 fis, clone KAT09018.
BC002777 - Homo sapiens exosome component 4, mRNA (cDNA clone MGC:3445 IMAGE:3613853), complete cds.
AB528720 - Synthetic construct DNA, clone: pF1KB6980, Homo sapiens EXOSC4 gene for exosome component 4, without stop codon, in Flexi system.
JF432617 - Synthetic construct Homo sapiens clone IMAGE:100073854 exosome component 4 (EXOSC4) gene, encodes complete protein.
KJ894034 - Synthetic construct Homo sapiens clone ccsbBroadEn_03428 EXOSC4 gene, encodes complete protein.

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

Reactome (by CSHL, EBI, and GO)

Protein Q9NPD3 (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: ENST00000316052.1, ENST00000316052.2, ENST00000316052.3, ENST00000316052.4, ENST00000316052.5, EXOS4_HUMAN, NM_019037, Q9NPD3, RRP41, SKI6, uc003zau.1, uc003zau.2, uc003zau.3, uc003zau.4, uc003zau.5
UCSC ID: ENST00000316052.6
RefSeq Accession: NM_019037
Protein: Q9NPD3 (aka EXOS4_HUMAN or RR41_HUMAN)
CCDS: CCDS6414.1

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