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Protein

Exosome complex exonuclease RRP42

Gene

Exosc7

Organism
Mus musculus (Mouse)
Status
Reviewed-Annotation score: Annotation score: 3 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 (By similarity).By similarity

GO - Molecular functioni

  1. RNA binding Source: UniProtKB-KW

GO - Biological processi

  1. rRNA processing Source: UniProtKB-KW
Complete GO annotation...

Keywords - Biological processi

rRNA processing

Keywords - Ligandi

RNA-binding

Enzyme and pathway databases

ReactomeiREACT_198696. KSRP destabilizes mRNA.
REACT_252013. mRNA decay by 3' to 5' exoribonuclease.

Names & Taxonomyi

Protein namesi
Recommended name:
Exosome complex exonuclease RRP42
Alternative name(s):
Exosome component 7
Ribosomal RNA-processing protein 42
Gene namesi
Name:Exosc7
Synonyms:Rrp42
OrganismiMus musculus (Mouse)
Taxonomic identifieri10090 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeMusMus
ProteomesiUP000000589: Chromosome 9

Organism-specific databases

MGIiMGI:1913696. Exosc7.

Subcellular locationi

Nucleusnucleolus By similarity. Cytoplasm By similarity. Nucleus By similarity

GO - Cellular componenti

  1. cytoplasm Source: UniProtKB-SubCell
  2. exosome (RNase complex) Source: UniProtKB
  3. nucleolus Source: UniProtKB-SubCell
  4. nucleus 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 – 291290Exosome complex exonuclease RRP42PRO_0000139964Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei2 – 21N-acetylalanineBy similarity
Modified residuei116 – 1161N6-acetyllysineBy similarity

Keywords - PTMi

Acetylation

Proteomic databases

MaxQBiQ9D0M0.
PaxDbiQ9D0M0.
PRIDEiQ9D0M0.

PTM databases

PhosphoSiteiQ9D0M0.

Expressioni

Gene expression databases

CleanExiMM_EXOSC7.
GenevestigatoriQ9D0M0.

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 EXOSC1 (By similarity). Interacts with ZC3HAV1 (By similarity).By similarity

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000026891.

Structurei

3D structure databases

ProteinModelPortaliQ9D0M0.
SMRiQ9D0M0. Positions 6-284.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Sequence similaritiesi

Belongs to the RNase PH family.Curated

Phylogenomic databases

eggNOGiCOG2123.
GeneTreeiENSGT00530000063093.
HOGENOMiHOG000229504.
HOVERGENiHBG051521.
InParanoidiQ9D0M0.
KOiK12589.
OMAiNVENVPC.
OrthoDBiEOG7H1JKZ.
TreeFamiTF320641.

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. 2 hits.
SSF55666. SSF55666. 1 hit.

Sequencei

Sequence statusi: Complete.

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

Q9D0M0-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MASVALSEAE KVYIVHGVQE DLRVDGRGCE DYRCVEVETD VVSNTSGSAR
60 70 80 90 100
VKLGHTDILV GVKAEMGTPK LEKPNEGYLE FFVDCSANAT PEFEGRGGDD
110 120 130 140 150
LGTEIANTLY RIFNNKSSVD LRSLCISPRE HCWVLYVDVL LLECGGNLFD
160 170 180 190 200
AISIAVKAAL FNTRIPRVRV LEDEEGAKDI ELSDDPYDCI RLSVENVPCI
210 220 230 240 250
VTLCKIGCRH VVDATLQEEA CSLASLLVSV TSKGVVTCMR KVGKGSLDPE
260 270 280 290
SIFEMMESSK RVGKVLHVSL QSLLHKEESL GPKRPRVGFL G
Length:291
Mass (Da):31,825
Last modified:October 3, 2012 - v2
Checksum:i74B52E4AF7BB52C5
GO

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK004437 mRNA. Translation: BAB23303.1.
AK011294 mRNA. No translation available.
AC134248 Genomic DNA. No translation available.
CH466587 Genomic DNA. Translation: EDL09072.1.
BC094932 mRNA. Translation: AAH94932.1.
BC132363 mRNA. Translation: AAI32364.1.
BC145675 mRNA. Translation: AAI45676.1.
CCDSiCCDS40815.1.
RefSeqiNP_001074657.1. NM_001081188.1.
UniGeneiMm.41562.

Genome annotation databases

EnsembliENSMUST00000026891; ENSMUSP00000026891; ENSMUSG00000025785.
GeneIDi66446.
KEGGimmu:66446.
UCSCiuc009sfv.1. mouse.

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AK004437 mRNA. Translation: BAB23303.1.
AK011294 mRNA. No translation available.
AC134248 Genomic DNA. No translation available.
CH466587 Genomic DNA. Translation: EDL09072.1.
BC094932 mRNA. Translation: AAH94932.1.
BC132363 mRNA. Translation: AAI32364.1.
BC145675 mRNA. Translation: AAI45676.1.
CCDSiCCDS40815.1.
RefSeqiNP_001074657.1. NM_001081188.1.
UniGeneiMm.41562.

3D structure databases

ProteinModelPortaliQ9D0M0.
SMRiQ9D0M0. Positions 6-284.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi10090.ENSMUSP00000026891.

PTM databases

PhosphoSiteiQ9D0M0.

Proteomic databases

MaxQBiQ9D0M0.
PaxDbiQ9D0M0.
PRIDEiQ9D0M0.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENSMUST00000026891; ENSMUSP00000026891; ENSMUSG00000025785.
GeneIDi66446.
KEGGimmu:66446.
UCSCiuc009sfv.1. mouse.

Organism-specific databases

CTDi23016.
MGIiMGI:1913696. Exosc7.

Phylogenomic databases

eggNOGiCOG2123.
GeneTreeiENSGT00530000063093.
HOGENOMiHOG000229504.
HOVERGENiHBG051521.
InParanoidiQ9D0M0.
KOiK12589.
OMAiNVENVPC.
OrthoDBiEOG7H1JKZ.
TreeFamiTF320641.

Enzyme and pathway databases

ReactomeiREACT_198696. KSRP destabilizes mRNA.
REACT_252013. mRNA decay by 3' to 5' exoribonuclease.

Miscellaneous databases

NextBioi321717.
PROiQ9D0M0.
SOURCEiSearch...

Gene expression databases

CleanExiMM_EXOSC7.
GenevestigatoriQ9D0M0.

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. 2 hits.
SSF55666. SSF55666. 1 hit.
ProtoNetiSearch...

Publicationsi

  1. "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].
    Strain: C57BL/6J.
    Tissue: Embryo.
  2. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
    Strain: C57BL/6J.
  3. Mural R.J., Adams M.D., Myers E.W., Smith H.O., Venter J.C.
    Submitted (JUL-2005) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. "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].
    Strain: 129/Sv X 129SvCp.
    Tissue: Brain and Embryonic stem cell.

Entry informationi

Entry nameiEXOS7_MOUSE
AccessioniPrimary (citable) accession number: Q9D0M0
Secondary accession number(s): Q4VBW5, Q9CT77
Entry historyi
Integrated into UniProtKB/Swiss-Prot: June 6, 2002
Last sequence update: October 3, 2012
Last modified: March 4, 2015
This is version 98 of the entry and version 2 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.