UniProtKB - Q9NPD3 (EXOS4_HUMAN)
Exosome complex component RRP41
EXOSC4
Functioni
Caution
GO - Molecular functioni
- 3'-5'-exoribonuclease activity Source: UniProtKB
- mRNA 3'-UTR AU-rich region binding Source: GO_Central
GO - Biological processi
- defense response to virus Source: MGI
- DNA deamination Source: UniProtKB
- exonucleolytic catabolism of deadenylated mRNA Source: Reactome
- histone mRNA catabolic process Source: UniProtKB
- maturation of 5.8S rRNA Source: UniProtKB
- nuclear mRNA surveillance Source: UniProtKB
- nuclear-transcribed mRNA catabolic process Source: UniProtKB
- nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: GO_Central
- polyadenylation-dependent snoRNA 3'-end processing Source: GO_Central
- positive regulation of cell growth Source: UniProtKB
- regulation of mRNA stability Source: Reactome
- rRNA catabolic process Source: GO_Central
- rRNA processing Source: Reactome
- U4 snRNA 3'-end processing Source: GO_Central
Keywordsi
Molecular function | RNA-binding |
Biological process | rRNA processing |
Enzyme and pathway databases
PathwayCommonsi | Q9NPD3 |
Reactomei | R-HSA-380994, ATF4 activates genes in response to endoplasmic reticulum stress R-HSA-429958, mRNA decay by 3' to 5' exoribonuclease R-HSA-450385, Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA R-HSA-450513, Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA R-HSA-450604, KSRP (KHSRP) binds and destabilizes mRNA R-HSA-6791226, Major pathway of rRNA processing in the nucleolus and cytosol |
SIGNORi | Q9NPD3 |
Protein family/group databases
MoonDBi | Q9NPD3, Predicted |
Names & Taxonomyi
Protein namesi | Recommended name: Exosome complex component RRP41Alternative name(s): Exosome component 4 Ribosomal RNA-processing protein 41 p12A |
Gene namesi | Name:EXOSC4 Synonyms:RRP41, SKI6 |
Organismi | Homo sapiens (Human) |
Taxonomic identifieri | 9606 [NCBI] |
Taxonomic lineagei | Eukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Primates › Haplorrhini › Catarrhini › Hominidae › Homo |
Proteomesi |
|
Organism-specific databases
HGNCi | HGNC:18189, EXOSC4 |
MIMi | 606491, gene |
neXtProti | NX_Q9NPD3 |
VEuPathDBi | HostDB:ENSG00000178896.6 |
Subcellular locationi
Cytosol
- cytosol Source: HPA
Nucleus
- nuclear exosome (RNase complex) Source: GO_Central
- nucleolus Source: GO_Central
- nucleoplasm Source: HPA
- nucleus Source: UniProtKB
Other locations
- cytoplasm Source: UniProtKB
- cytoplasmic exosome (RNase complex) Source: GO_Central
- exosome (RNase complex) Source: UniProtKB
- intracellular membrane-bounded organelle Source: HPA
- transcriptionally active chromatin Source: UniProtKB
Keywords - Cellular componenti
Cytoplasm, Exosome, NucleusPathology & Biotechi
Organism-specific databases
DisGeNETi | 54512 |
OpenTargetsi | ENSG00000178896 |
PharmGKBi | PA134867931 |
Miscellaneous databases
Pharosi | Q9NPD3, Tbio |
Genetic variation databases
BioMutai | EXOSC4 |
DMDMi | 14285756 |
PTM / Processingi
Molecule processing
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Initiator methioninei | RemovedCombined sources1 Publication | |||
ChainiPRO_0000139958 | 2 – 245 | Exosome complex component RRP41Add BLAST | 244 |
Amino acid modifications
Feature key | Position(s) | DescriptionActions | Graphical view | Length |
---|---|---|---|---|
Modified residuei | 2 | N-acetylalanineCombined sources1 Publication | 1 |
Keywords - PTMi
AcetylationProteomic databases
EPDi | Q9NPD3 |
jPOSTi | Q9NPD3 |
MassIVEi | Q9NPD3 |
MaxQBi | Q9NPD3 |
PaxDbi | Q9NPD3 |
PeptideAtlasi | Q9NPD3 |
PRIDEi | Q9NPD3 |
ProteomicsDBi | 81973 |
2D gel databases
SWISS-2DPAGEi | Q9NPD3 |
PTM databases
iPTMneti | Q9NPD3 |
MetOSitei | Q9NPD3 |
PhosphoSitePlusi | Q9NPD3 |
SwissPalmi | Q9NPD3 |
Expressioni
Gene expression databases
Bgeei | ENSG00000178896, Expressed in left testis and 166 other tissues |
ExpressionAtlasi | Q9NPD3, baseline and differential |
Genevisiblei | Q9NPD3, HS |
Organism-specific databases
HPAi | ENSG00000178896, Low tissue specificity |
Interactioni
Subunit structurei
Component of the RNA exosome complex (PubMed:29906447). 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.
4 PublicationsBinary interactionsi
Hide detailsQ9NPD3
Protein-protein interaction databases
BioGRIDi | 120007, 141 interactors |
ComplexPortali | CPX-476, Nuclear exosome complex, DIS3-EXOSC10 variant CPX-591, Nucleolar exosome complex, EXOSC10 variant CPX-592, Cytoplasmic exosome complex, DIS3L variant CPX-593, Exosome complex, DIS3 variant CPX-600, Cytoplasmic exosome complex, DIS3L-EXOSC10 variant |
CORUMi | Q9NPD3 |
DIPi | DIP-31165N |
IntActi | Q9NPD3, 70 interactors |
MINTi | Q9NPD3 |
STRINGi | 9606.ENSP00000315476 |
Miscellaneous databases
RNActi | Q9NPD3, protein |
Structurei
Secondary structure
3D structure databases
SMRi | Q9NPD3 |
ModBasei | Search... |
PDBe-KBi | Search... |
Miscellaneous databases
EvolutionaryTracei | Q9NPD3 |
Family & Domainsi
Sequence similaritiesi
Phylogenomic databases
eggNOGi | KOG1068, Eukaryota |
GeneTreei | ENSGT00940000153348 |
HOGENOMi | CLU_063514_0_0_1 |
InParanoidi | Q9NPD3 |
OMAi | CYAEESG |
OrthoDBi | 1394468at2759 |
PhylomeDBi | Q9NPD3 |
TreeFami | TF313915 |
Family and domain databases
Gene3Di | 3.30.230.70, 1 hit |
InterProi | View protein in InterPro IPR001247, ExoRNase_PH_dom1 IPR015847, ExoRNase_PH_dom2 IPR036345, ExoRNase_PH_dom2_sf IPR027408, PNPase/RNase_PH_dom_sf IPR020568, Ribosomal_S5_D2-typ_fold |
Pfami | View protein in Pfam PF01138, RNase_PH, 1 hit PF03725, RNase_PH_C, 1 hit |
SUPFAMi | SSF54211, SSF54211, 1 hit SSF55666, SSF55666, 1 hit |
(1+)i Sequence
Sequence statusi: Complete.
: The displayed sequence is further processed into a mature form. Sequence processingi
This entry has 1 described isoform and 2 potential isoforms that are computationally mapped.Show allAlign All
10 20 30 40 50
MAGLELLSDQ GYRVDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA
60 70 80 90 100
VVYGPHEIRG SRARALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG
110 120 130 140 150
LQLRQTFEAA ILTQLHPRSQ IDIYVQVLQA DGGTYAACVN AATLAVLDAG
160 170 180 190 200
IPMRDFVCAC SAGFVDGTAL ADLSHVEEAA GGPQLALALL PASGQIALLE
210 220 230 240
MDARLHEDHL ERVLEAAAQA ARDVHTLLDR VVRQHVREAS ILLGD
Computationally mapped potential isoform sequencesi
There are 2 potential isoforms mapped to this entry.BLASTAlignShow allAdd to basketE9PI41 | E9PI41_HUMAN | Exosome complex component RRP41 | EXOSC4 | 261 | Annotation score: | ||
E9PPI9 | E9PPI9_HUMAN | Exosome complex component RRP41 | EXOSC4 | 156 | Annotation score: |
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF281133 mRNA Translation: AAF82134.1 AK000598 mRNA Translation: BAA91279.1 AC109322 Genomic DNA No translation available. BC002777 mRNA Translation: AAH02777.1 |
CCDSi | CCDS6414.1 |
RefSeqi | NP_061910.1, NM_019037.2 |
Genome annotation databases
Ensembli | ENST00000316052; ENSP00000315476; ENSG00000178896 |
GeneIDi | 54512 |
KEGGi | hsa:54512 |
UCSCi | uc003zau.4, human |
Similar proteinsi
Cross-referencesi
Sequence databases
Select the link destinations: EMBLi GenBanki DDBJi Links Updated | AF281133 mRNA Translation: AAF82134.1 AK000598 mRNA Translation: BAA91279.1 AC109322 Genomic DNA No translation available. BC002777 mRNA Translation: AAH02777.1 |
CCDSi | CCDS6414.1 |
RefSeqi | NP_061910.1, NM_019037.2 |
3D structure databases
Select the link destinations: PDBei RCSB PDBi PDBji Links Updated | PDB entry | Method | Resolution (Å) | Chain | Positions | PDBsum |
2NN6 | X-ray | 3.35 | B | 2-245 | [»] | |
6D6Q | electron microscopy | 3.45 | B | 1-245 | [»] | |
6D6R | electron microscopy | 3.45 | B | 1-245 | [»] | |
6H25 | electron microscopy | 3.80 | B | 1-245 | [»] | |
SMRi | Q9NPD3 | |||||
ModBasei | Search... | |||||
PDBe-KBi | Search... |
Protein-protein interaction databases
BioGRIDi | 120007, 141 interactors |
ComplexPortali | CPX-476, Nuclear exosome complex, DIS3-EXOSC10 variant CPX-591, Nucleolar exosome complex, EXOSC10 variant CPX-592, Cytoplasmic exosome complex, DIS3L variant CPX-593, Exosome complex, DIS3 variant CPX-600, Cytoplasmic exosome complex, DIS3L-EXOSC10 variant |
CORUMi | Q9NPD3 |
DIPi | DIP-31165N |
IntActi | Q9NPD3, 70 interactors |
MINTi | Q9NPD3 |
STRINGi | 9606.ENSP00000315476 |
Protein family/group databases
MoonDBi | Q9NPD3, Predicted |
PTM databases
iPTMneti | Q9NPD3 |
MetOSitei | Q9NPD3 |
PhosphoSitePlusi | Q9NPD3 |
SwissPalmi | Q9NPD3 |
Genetic variation databases
BioMutai | EXOSC4 |
DMDMi | 14285756 |
2D gel databases
SWISS-2DPAGEi | Q9NPD3 |
Proteomic databases
EPDi | Q9NPD3 |
jPOSTi | Q9NPD3 |
MassIVEi | Q9NPD3 |
MaxQBi | Q9NPD3 |
PaxDbi | Q9NPD3 |
PeptideAtlasi | Q9NPD3 |
PRIDEi | Q9NPD3 |
ProteomicsDBi | 81973 |
Protocols and materials databases
Antibodypediai | 14755, 169 antibodies |
DNASUi | 54512 |
Genome annotation databases
Ensembli | ENST00000316052; ENSP00000315476; ENSG00000178896 |
GeneIDi | 54512 |
KEGGi | hsa:54512 |
UCSCi | uc003zau.4, human |
Organism-specific databases
CTDi | 54512 |
DisGeNETi | 54512 |
GeneCardsi | EXOSC4 |
HGNCi | HGNC:18189, EXOSC4 |
HPAi | ENSG00000178896, Low tissue specificity |
MIMi | 606491, gene |
neXtProti | NX_Q9NPD3 |
OpenTargetsi | ENSG00000178896 |
PharmGKBi | PA134867931 |
VEuPathDBi | HostDB:ENSG00000178896.6 |
GenAtlasi | Search... |
Phylogenomic databases
eggNOGi | KOG1068, Eukaryota |
GeneTreei | ENSGT00940000153348 |
HOGENOMi | CLU_063514_0_0_1 |
InParanoidi | Q9NPD3 |
OMAi | CYAEESG |
OrthoDBi | 1394468at2759 |
PhylomeDBi | Q9NPD3 |
TreeFami | TF313915 |
Enzyme and pathway databases
PathwayCommonsi | Q9NPD3 |
Reactomei | R-HSA-380994, ATF4 activates genes in response to endoplasmic reticulum stress R-HSA-429958, mRNA decay by 3' to 5' exoribonuclease R-HSA-450385, Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA R-HSA-450513, Tristetraprolin (TTP, ZFP36) binds and destabilizes mRNA R-HSA-450604, KSRP (KHSRP) binds and destabilizes mRNA R-HSA-6791226, Major pathway of rRNA processing in the nucleolus and cytosol |
SIGNORi | Q9NPD3 |
Miscellaneous databases
BioGRID-ORCSi | 54512, 749 hits in 973 CRISPR screens |
ChiTaRSi | EXOSC4, human |
EvolutionaryTracei | Q9NPD3 |
GeneWikii | Exosome_component_4 |
GenomeRNAii | 54512 |
Pharosi | Q9NPD3, Tbio |
PROi | PR:Q9NPD3 |
RNActi | Q9NPD3, protein |
SOURCEi | Search... |
Gene expression databases
Bgeei | ENSG00000178896, Expressed in left testis and 166 other tissues |
ExpressionAtlasi | Q9NPD3, baseline and differential |
Genevisiblei | Q9NPD3, HS |
Family and domain databases
Gene3Di | 3.30.230.70, 1 hit |
InterProi | View protein in InterPro IPR001247, ExoRNase_PH_dom1 IPR015847, ExoRNase_PH_dom2 IPR036345, ExoRNase_PH_dom2_sf IPR027408, PNPase/RNase_PH_dom_sf IPR020568, Ribosomal_S5_D2-typ_fold |
Pfami | View protein in Pfam PF01138, RNase_PH, 1 hit PF03725, RNase_PH_C, 1 hit |
SUPFAMi | SSF54211, SSF54211, 1 hit SSF55666, SSF55666, 1 hit |
ProtoNeti | Search... |
MobiDBi | Search... |
Entry informationi
Entry namei | EXOS4_HUMAN | |
Accessioni | Q9NPD3Primary (citable) accession number: Q9NPD3 | |
Entry historyi | Integrated into UniProtKB/Swiss-Prot: | June 1, 2001 |
Last sequence update: | January 23, 2007 | |
Last modified: | April 7, 2021 | |
This is version 189 of the entry and version 3 of the sequence. See complete history. | ||
Entry statusi | Reviewed (UniProtKB/Swiss-Prot) | |
Annotation program | Chordata Protein Annotation Program | |
Disclaimer | Any medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care. |
Miscellaneousi
Keywords - Technical termi
3D-structure, Direct protein sequencing, Reference proteomeDocuments
- Human chromosome 8
Human chromosome 8: entries, gene names and cross-references to MIM - MIM cross-references
Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot - PDB cross-references
Index of Protein Data Bank (PDB) cross-references - SIMILARITY comments
Index of protein domains and families