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Protein

Exosome complex component RRP40

Gene

Exosc3

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein 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. EXOSC3 as peripheral part of the Exo-9 complex stabilizes the hexameric ring of RNase PH-domain subunits through contacts with EXOSC9 and EXOSC5 (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

ReactomeiREACT_288807. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_291652. mRNA decay by 3' to 5' exoribonuclease.
REACT_300665. KSRP destabilizes mRNA.
REACT_307913. Tristetraprolin (TTP) destabilizes mRNA.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex component RRP40 (EC:3.1.13.-)
Alternative name(s):
Exosome component 3
Ribosomal RNA-processing protein 40
Gene namesi
Name:Exosc3
Synonyms:Rrp40
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589 Componenti: Chromosome 4

Organism-specific databases

MGIiMGI:1913612. Exosc3.

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 methioninei1 – 11RemovedBy similarity
Chaini2 – 274273Exosome complex component RRP40PRO_0000087132Add
BLAST

Amino acid modifications

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

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ7TQK4.
PaxDbiQ7TQK4.
PRIDEiQ7TQK4.

PTM databases

PhosphoSiteiQ7TQK4.

Expressioni

Gene expression databases

BgeeiQ7TQK4.
CleanExiMM_EXOSC3.
GenevestigatoriQ7TQK4.

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. Interacts with GTPBP1 (By similarity). Interacts with ZC3HAV1 (By similarity). Interacts with DDX17 only in the presence of ZC3HAV1 in an RNA-independent manner (By similarity).By similarity

Protein-protein interaction databases

IntActiQ7TQK4. 2 interactions.
MINTiMINT-4094772.

Structurei

3D structure databases

ProteinModelPortaliQ7TQK4.
SMRiQ7TQK4. Positions 17-274.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RRP40 family.Curated

Phylogenomic databases

eggNOGiCOG1097.
GeneTreeiENSGT00390000012042.
HOGENOMiHOG000184644.
HOVERGENiHBG051518.
InParanoidiQ7TQK4.
KOiK03681.
OMAiHKEPGSG.
OrthoDBiEOG76HQ2F.
PhylomeDBiQ7TQK4.
TreeFamiTF314927.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q7TQK4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MAEVLSAGPE SVAGCRARAV HKVLNQVVLP GEELVLPDHE DVDGLGGAGE
60 70 80 90 100
QPLRLNAGAR PRLRVVCGPG LRRCGDRLLV TKCGRLRHKE PSGGGGGVYW
110 120 130 140 150
VDSQQKRYVP VKGDHVIGIV IAKSGDIFKV DVGGSEPASL SYLAFEGATK
160 170 180 190 200
RNRPNVQVGD LIYGQCVVAN KDMEPEMVCI DSCGRANGMG VIGQDGLLFK
210 220 230 240 250
VTLGLIRKLL APDCEIVQEL GKLYPLEIVF GMNGRIWVKA KTIQQTLILA
260 270
NVLEACEHMT TEQRKQIFAR LAES
Length:274
Mass (Da):29,546
Last modified:January 23, 2007 - v3
Checksum:i0932E5B03DD708D4
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti32 – 321E → P in BAB24501 (PubMed:16141072).Curated

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC023669 mRNA. Translation: AAH23669.1.
BC054085 mRNA. Translation: AAH54085.1.
AK006281 mRNA. Translation: BAB24501.1.
AK009165 mRNA. Translation: BAB26116.1.
CCDSiCCDS18136.1.
RefSeqiNP_079789.1. NM_025513.3.
UniGeneiMm.275788.

Genome annotation databases

EnsembliENSMUST00000030003; ENSMUSP00000030003; ENSMUSG00000028322.
GeneIDi66362.
KEGGimmu:66362.
UCSCiuc008ssk.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
BC023669 mRNA. Translation: AAH23669.1.
BC054085 mRNA. Translation: AAH54085.1.
AK006281 mRNA. Translation: BAB24501.1.
AK009165 mRNA. Translation: BAB26116.1.
CCDSiCCDS18136.1.
RefSeqiNP_079789.1. NM_025513.3.
UniGeneiMm.275788.

3D structure databases

ProteinModelPortaliQ7TQK4.
SMRiQ7TQK4. Positions 17-274.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

IntActiQ7TQK4. 2 interactions.
MINTiMINT-4094772.

PTM databases

PhosphoSiteiQ7TQK4.

Proteomic databases

MaxQBiQ7TQK4.
PaxDbiQ7TQK4.
PRIDEiQ7TQK4.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000030003; ENSMUSP00000030003; ENSMUSG00000028322.
GeneIDi66362.
KEGGimmu:66362.
UCSCiuc008ssk.1. mouse.

Organism-specific databases

CTDi51010.
MGIiMGI:1913612. Exosc3.

Phylogenomic databases

eggNOGiCOG1097.
GeneTreeiENSGT00390000012042.
HOGENOMiHOG000184644.
HOVERGENiHBG051518.
InParanoidiQ7TQK4.
KOiK03681.
OMAiHKEPGSG.
OrthoDBiEOG76HQ2F.
PhylomeDBiQ7TQK4.
TreeFamiTF314927.

Enzyme and pathway databases

ReactomeiREACT_288807. Butyrate Response Factor 1 (BRF1) destabilizes mRNA.
REACT_291652. mRNA decay by 3' to 5' exoribonuclease.
REACT_300665. KSRP destabilizes mRNA.
REACT_307913. Tristetraprolin (TTP) destabilizes mRNA.

Miscellaneous databases

ChiTaRSiExosc3. mouse.
NextBioi321447.
PROiQ7TQK4.
SOURCEiSearch...

Gene expression databases

BgeeiQ7TQK4.
CleanExiMM_EXOSC3.
GenevestigatoriQ7TQK4.

Family and domain databases

InterProiIPR026699. Exosome_RNA_bind1/RRP40/RRP4.
IPR004088. KH_dom_type_1.
IPR012340. NA-bd_OB-fold.
[Graphical view]
PANTHERiPTHR21321. PTHR21321. 1 hit.
SUPFAMiSSF50249. SSF50249. 1 hit.
SSF54791. SSF54791. 1 hit.
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  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].
    Tissue: Mammary gland.
  2. "The transcriptional landscape of the mammalian genome."
    Carninci P., Kasukawa T., Katayama S., Gough J., Frith M.C., Maeda N., Oyama R., Ravasi T., Lenhard B., Wells C., Kodzius R., Shimokawa K., Bajic V.B., Brenner S.E., Batalov S., Forrest A.R., Zavolan M., Davis M.J.
    , Wilming L.G., Aidinis V., Allen J.E., Ambesi-Impiombato A., Apweiler R., Aturaliya R.N., Bailey T.L., Bansal M., Baxter L., Beisel K.W., Bersano T., Bono H., Chalk A.M., Chiu K.P., Choudhary V., Christoffels A., Clutterbuck D.R., Crowe M.L., Dalla E., Dalrymple B.P., de Bono B., Della Gatta G., di Bernardo D., Down T., Engstrom P., Fagiolini M., Faulkner G., Fletcher C.F., Fukushima T., Furuno M., Futaki S., Gariboldi M., Georgii-Hemming P., Gingeras T.R., Gojobori T., Green R.E., Gustincich S., Harbers M., Hayashi Y., Hensch T.K., Hirokawa N., Hill D., Huminiecki L., Iacono M., Ikeo K., Iwama A., Ishikawa T., Jakt M., Kanapin A., Katoh M., Kawasawa Y., Kelso J., Kitamura H., Kitano H., Kollias G., Krishnan S.P., Kruger A., Kummerfeld S.K., Kurochkin I.V., Lareau L.F., Lazarevic D., Lipovich L., Liu J., Liuni S., McWilliam S., Madan Babu M., Madera M., Marchionni L., Matsuda H., Matsuzawa S., Miki H., Mignone F., Miyake S., Morris K., Mottagui-Tabar S., Mulder N., Nakano N., Nakauchi H., Ng P., Nilsson R., Nishiguchi S., Nishikawa S., Nori F., Ohara O., Okazaki Y., Orlando V., Pang K.C., Pavan W.J., Pavesi G., Pesole G., Petrovsky N., Piazza S., Reed J., Reid J.F., Ring B.Z., Ringwald M., Rost B., Ruan Y., Salzberg S.L., Sandelin A., Schneider C., Schoenbach C., Sekiguchi K., Semple C.A., Seno S., Sessa L., Sheng Y., Shibata Y., Shimada H., Shimada K., Silva D., Sinclair B., Sperling S., Stupka E., Sugiura K., Sultana R., Takenaka Y., Taki K., Tammoja K., Tan S.L., Tang S., Taylor M.S., Tegner J., Teichmann S.A., Ueda H.R., van Nimwegen E., Verardo R., Wei C.L., Yagi K., Yamanishi H., Zabarovsky E., Zhu S., Zimmer A., Hide W., Bult C., Grimmond S.M., Teasdale R.D., Liu E.T., Brusic V., Quackenbush J., Wahlestedt C., Mattick J.S., Hume D.A., Kai C., Sasaki D., Tomaru Y., Fukuda S., Kanamori-Katayama M., Suzuki M., Aoki J., Arakawa T., Iida J., Imamura K., Itoh M., Kato T., Kawaji H., Kawagashira N., Kawashima T., Kojima M., Kondo S., Konno H., Nakano K., Ninomiya N., Nishio T., Okada M., Plessy C., Shibata K., Shiraki T., Suzuki S., Tagami M., Waki K., Watahiki A., Okamura-Oho Y., Suzuki H., Kawai J., Hayashizaki Y.
    Science 309:1559-1563(2005) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] OF 32-274.
    Strain: C57BL/6J.
    Tissue: Testis and Tongue.
  3. "The RNA exosome targets the AID cytidine deaminase to both strands of transcribed duplex DNA substrates."
    Basu U., Meng F.L., Keim C., Grinstein V., Pefanis E., Eccleston J., Zhang T., Myers D., Wasserman C.R., Wesemann D.R., Januszyk K., Gregory R.I., Deng H., Lima C.D., Alt F.W.
    Cell 144:353-363(2011) [PubMed] [Europe PMC] [Abstract]
    Cited for: FUNCTION IN IG CLASS-SWITCH.

Entry informationi

Entry nameiEXOS3_MOUSE
AccessioniPrimary (citable) accession number: Q7TQK4
Secondary accession number(s): Q9CV81, Q9CVW2
Entry historyi
Integrated into UniProtKB/Swiss-Prot: April 26, 2004
Last sequence update: January 23, 2007
Last modified: May 27, 2015
This is version 95 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.