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Protein

Exosome complex component RRP41

Gene

Exosc4

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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 (By similarity).By similarity

GO - Molecular functioni

  1. AU-rich element binding Source: MGI

GO - Biological processi

  1. defense response to virus Source: MGI
  2. DNA deamination Source: MGI
  3. histone mRNA catabolic process Source: UniProtKB
  4. maturation of 5.8S rRNA Source: MGI
  5. nuclear mRNA surveillance Source: MGI
  6. nuclear-transcribed mRNA catabolic process Source: MGI
  7. nuclear-transcribed mRNA catabolic process, exonucleolytic, 3'-5' Source: GO_Central
  8. polyadenylation-dependent snoRNA 3'-end processing Source: GO_Central
  9. positive regulation of cell growth Source: MGI
  10. rRNA 3'-end processing Source: GO_Central
  11. rRNA catabolic process Source: GO_Central
  12. U4 snRNA 3'-end processing Source: GO_Central
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_291652. mRNA decay by 3' to 5' exoribonuclease.
REACT_300665. KSRP destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP41
Alternative name(s):
Exosome component 4
Ribosomal RNA-processing protein 41
Gene namesi
Name:Exosc4
Synonyms:Rrp41
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 15

Organism-specific databases

MGIiMGI:1923576. Exosc4.

Subcellular locationi

  1. Cytoplasm By similarity
  2. Nucleusnucleolus By similarity
  3. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: MGI
  2. cytoplasmic exosome (RNase complex) Source: GO_Central
  3. exosome (RNase complex) Source: UniProtKB
  4. nuclear exosome (RNase complex) Source: GO_Central
  5. nucleolus Source: GO_Central
  6. nucleus Source: MGI
  7. transcriptionally active chromatin Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methioninei1 – 11RemovedBy similarity
Chaini2 – 245244Exosome complex component RRP41PRO_0000139959Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ921I9.
PaxDbiQ921I9.
PRIDEiQ921I9.

PTM databases

PhosphoSiteiQ921I9.

Expressioni

Gene expression databases

BgeeiQ921I9.
CleanExiMM_EXOSC4.
ExpressionAtlasiQ921I9. baseline and differential.
GenevestigatoriQ921I9.

Interactioni

Subunit structurei

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 (By similarity). Interacts with DDX60 (By similarity).By similarity

Protein-protein interaction databases

BioGridi224543. 2 interactions.
IntActiQ921I9. 1 interaction.
MINTiMINT-4094786.

Structurei

3D structure databases

ProteinModelPortaliQ921I9.
SMRiQ921I9. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiCOG0689.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ921I9.
KOiK11600.
OMAiDITLLQM.
OrthoDBiEOG74J98C.
PhylomeDBiQ921I9.
TreeFamiTF313915.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

Sequence processingi: The displayed sequence is further processed into a mature form.

Q921I9-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAGLELLSDQ GYRIDGRRAG ELRKIQARMG VFAQADGSAY IEQGNTKALA
60 70 80 90 100
VVYGPHEIRG SRSRALPDRA LVNCQYSSAT FSTGERKRRP HGDRKSCEMG
110 120 130 140 150
LQLRQTFEAA ILTQLHPRSQ IDIYVQVLQA DGGTYAACVN AATLAVMDAG
160 170 180 190 200
IPMRDFVCAC SAGFVDGTAL ADLSHVEEAA GGPQLALALL PASGQIALLE
210 220 230 240
MDSRLHEDHL EQVLEAAAQA ARGVHTLLDL VVRQHVQEAS VSLGD
Length:245
Mass (Da):26,250
Last modified:January 23, 2007 - v3
Checksum:iE06C1CA2CA1FBF57
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC012277 mRNA. Translation: AAH12277.1.
CCDSiCCDS37119.1.
RefSeqiNP_780608.1. NM_175399.4.
UniGeneiMm.322752.

Genome annotation databases

EnsembliENSMUST00000059045; ENSMUSP00000050940; ENSMUSG00000034259.
GeneIDi109075.
KEGGimmu:109075.
UCSCiuc007wjp.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC012277 mRNA. Translation: AAH12277.1.
CCDSiCCDS37119.1.
RefSeqiNP_780608.1. NM_175399.4.
UniGeneiMm.322752.

3D structure databases

ProteinModelPortaliQ921I9.
SMRiQ921I9. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi224543. 2 interactions.
IntActiQ921I9. 1 interaction.
MINTiMINT-4094786.

PTM databases

PhosphoSiteiQ921I9.

Proteomic databases

MaxQBiQ921I9.
PaxDbiQ921I9.
PRIDEiQ921I9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000059045; ENSMUSP00000050940; ENSMUSG00000034259.
GeneIDi109075.
KEGGimmu:109075.
UCSCiuc007wjp.1. mouse.

Organism-specific databases

CTDi54512.
MGIiMGI:1923576. Exosc4.

Phylogenomic databases

eggNOGiCOG0689.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ921I9.
KOiK11600.
OMAiDITLLQM.
OrthoDBiEOG74J98C.
PhylomeDBiQ921I9.
TreeFamiTF313915.

Enzyme and pathway databases

ReactomeiREACT_291652. mRNA decay by 3' to 5' exoribonuclease.
REACT_300665. KSRP destabilizes mRNA.

Miscellaneous databases

ChiTaRSiExosc4. mouse.
NextBioi361620.
PROiQ921I9.
SOURCEiSearch...

Gene expression databases

BgeeiQ921I9.
CleanExiMM_EXOSC4.
ExpressionAtlasiQ921I9. baseline and differential.
GenevestigatoriQ921I9.

Family and domain databases

Gene3Di3.30.230.70. 1 hit.
InterProiIPR001247. ExoRNase_PH_dom1.
IPR015847. ExoRNase_PH_dom2.
IPR027408. PNPase/RNase_PH_dom.
IPR020568. Ribosomal_S5_D2-typ_fold.
[Graphical view]
PfamiPF01138. RNase_PH. 1 hit.
PF03725. RNase_PH_C. 1 hit.
[Graphical view]
SUPFAMiSSF54211. SSF54211. 1 hit.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].

Entry informationi

Entry nameiEXOS4_MOUSE
AccessioniPrimary (citable) accession number: Q921I9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: July 11, 2002
Last sequence update: January 23, 2007
Last modified: April 29, 2015
This is version 109 of the entry and version 3 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. MGD cross-references
    Mouse Genome Database (MGD) cross-references in UniProtKB/Swiss-Prot
  2. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.