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Protein

Exosome complex component RRP41

Gene

EXOSC4

Organism
Bos taurus (Bovine)
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

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Exonuclease, Hydrolase, Nuclease

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiR-BTA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-BTA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-BTA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-BTA-6791226. Major pathway of rRNA processing in the nucleolus.

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
OrganismiBos taurus (Bovine)
Taxonomic identifieri9913 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaLaurasiatheriaCetartiodactylaRuminantiaPecoraBovidaeBovinaeBos
Proteomesi
  • UP000009136 Componenti: Chromosome 14

Subcellular locationi

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Exosome, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Initiator methionineiRemovedBy similarity
Chaini2 – 245244Exosome complex component RRP41PRO_0000259642Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation

Proteomic databases

PaxDbiQ7YRA3.
PRIDEiQ7YRA3.

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

STRINGi9913.ENSBTAP00000019451.

Structurei

3D structure databases

ProteinModelPortaliQ7YRA3.
SMRiQ7YRA3. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ7YRA3.
KOiK11600.
OMAiFKMYLQQ.
OrthoDBiEOG74J98C.
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.

Q7YRA3-1 [UniParc]FASTAAdd to basket

« Hide

        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 EQVLEAAARA SRDVHTVLDR VVRQHVQEAS VLLGD
Length:245
Mass (Da):26,343
Last modified:January 23, 2007 - v3
Checksum:i6AC835BD064AF313
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti70 – 701A → P in AAI09820 (Ref. 2) Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ518955 Genomic DNA. Translation: CAD58792.1.
BC109819 mRNA. Translation: AAI09820.1.
RefSeqiNP_001071554.1. NM_001078086.2.
UniGeneiBt.16597.

Genome annotation databases

EnsembliENSBTAT00000019451; ENSBTAP00000019451; ENSBTAG00000014607.
GeneIDi618292.
KEGGibta:618292.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AJ518955 Genomic DNA. Translation: CAD58792.1.
BC109819 mRNA. Translation: AAI09820.1.
RefSeqiNP_001071554.1. NM_001078086.2.
UniGeneiBt.16597.

3D structure databases

ProteinModelPortaliQ7YRA3.
SMRiQ7YRA3. Positions 7-241.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9913.ENSBTAP00000019451.

Proteomic databases

PaxDbiQ7YRA3.
PRIDEiQ7YRA3.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSBTAT00000019451; ENSBTAP00000019451; ENSBTAG00000014607.
GeneIDi618292.
KEGGibta:618292.

Organism-specific databases

CTDi54512.

Phylogenomic databases

eggNOGiKOG1068. Eukaryota.
COG0689. LUCA.
GeneTreeiENSGT00550000074804.
HOGENOMiHOG000229515.
HOVERGENiHBG051519.
InParanoidiQ7YRA3.
KOiK11600.
OMAiFKMYLQQ.
OrthoDBiEOG74J98C.
TreeFamiTF313915.

Enzyme and pathway databases

ReactomeiR-BTA-429958. mRNA decay by 3' to 5' exoribonuclease.
R-BTA-450385. Butyrate Response Factor 1 (BRF1) binds and destabilizes mRNA.
R-BTA-450604. KSRP (KHSRP) binds and destabilizes mRNA.
R-BTA-6791226. Major pathway of rRNA processing in the nucleolus.

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

« Hide 'large scale' publications
  1. "Assessment of the gene content of the chromosomal regions flanking bovine DGAT1."
    Winter A., Alzinger A., Fries R.
    Genomics 83:172-180(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [GENOMIC DNA].
  2. NIH - Mammalian Gene Collection (MGC) project
    Submitted (NOV-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA].
    Strain: Crossbred X Angus.
    Tissue: Liver.

Entry informationi

Entry nameiEXOS4_BOVIN
AccessioniPrimary (citable) accession number: Q7YRA3
Secondary accession number(s): Q32L11
Entry historyi
Integrated into UniProtKB/Swiss-Prot: October 31, 2006
Last sequence update: January 23, 2007
Last modified: June 8, 2016
This is version 89 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. SIMILARITY comments
    Index of protein domains and families

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 one 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.