protein coding gene - rrp4 (SPAC2F7.14c) - exosome subunit Rrp4

Gene summary

Standard name: rrp4
Systematic ID: SPAC2F7.14c
Product: exosome subunit Rrp4
Organism: Schizosaccharomyces pombe (fission yeast)
UniProt ID: Q09704
ORFeome ID: 14/14D02
Characterisation status: biological role published
Feature type: mRNA gene
Genomic location: chromosome I: 560824..562161 reverse strand

Annotation

Disease association

MONDO:0044634 - retinitis pigmentosa-hearing loss-premature aging-short stature-facial dysmorphism syndrome

References:

GO biological process

GO:0071034 - CUT catabolic process

References:

GO_REF:0000033

GO:0000467 - exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

References:

GO_REF:0000033

GO:0070651 - nonfunctional rRNA decay

References:

GO_REF:0000024

GO:0071028 - nuclear mRNA surveillance

References:

PMID:25240800

GO:0071042 - nuclear polyadenylation-dependent mRNA catabolic process

References:

GO_REF:0000024

GO:0071035 - nuclear polyadenylation-dependent rRNA catabolic process

References:

GO_REF:0000033

GO:0070478 - nuclear-transcribed mRNA catabolic process, 3'-5' exonucleolytic nonsense-mediated decay

References:

GO_REF:0000024

GO:0070481 - nuclear-transcribed mRNA catabolic process, non-stop decay

References:

GO_REF:0000024

GO:0071051 - poly(A)-dependent snoRNA 3'-end processing

References:

GO_REF:0000033

GO:0071038 - TRAMP-dependent tRNA surveillance pathway

References:

GO_REF:0000033

GO:0034475 - U4 snRNA 3'-end processing

References:

GO_REF:0000033

GO cellular component

GO:0000785 - chromatin

References:

PMID:25240800

GO:0000177 - cytoplasmic exosome (RNase complex)

References:

GO_REF:0000033

GO:0005829 - cytosol

References:

PMID:16823372

GO:0000178 - exosome (RNase complex)

References:

PMID:23503588

GO:0000176 - nuclear exosome (RNase complex)

References:

PMID:29906447

GO:0005634 - nucleus

References:

PMID:16823372

GO molecular function

GO:0003723 - RNA binding

References:

GO_REF:0000033

Modification

MOD:00046 - O-phospho-L-serine

References:

PMID:30726745

MOD:01148 - ubiquitinylated lysine

References:

PMID:37970674

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PMID:39705284

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

PMID:23101633

Single locus phenotype

FYPO:0000059 - abnormal mitotic cell cycle

References:

PMID:23697806

Genotypes:

rrp4delta

FYPO:0000314 - inviable after spore germination with elongated germ tube

References:

PMID:23697806

Genotypes:

rrp4delta

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

rrp4delta

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

PBO:0011071 - conserved in eukaryotes only

PBO:0011064 - conserved in fungi

PBO:0011069 - conserved in metazoa

PBO:0011070 - conserved in vertebrates

PBO:0006222 - predominantly single copy (one to one)

Protein features

ID	Name	InterPro name	DB name
PF14382	ECR1_N	Exosome_cplx_N_dom	Pfam
PF15985	KH_6	KH_dom_type_1	Pfam
PF21266	S1_RRP4	S1_RRP4	Pfam
cd05789	S1_Rrp4	S1_RRP4	CDD
cd22525	KH-I_Rrp4_eukar		CDD
SM00316	S1	S1_domain	SMART
G3DSA:2.40.50.140:FF:000038			CATH-FunFam
G3DSA:2.40.50.100			CATH-Gene3D
G3DSA:2.40.50.140		NA-bd_OB-fold	CATH-Gene3D
SSF110324			SUPERFAMILY
SSF50249		NA-bd_OB-fold	SUPERFAMILY
SSF54791		KH_dom_type_1_sf	SUPERFAMILY
PTHR21321		Exosome_RNA_bind1/RRP40/RRP4	PANTHER

Orthologs

EXOSC2 (HGNC:17097) Homo sapiens
rrp4 (SJAG_01521) Schizosaccharomyces japonicus
RRP4 (YHR069C) Saccharomyces cerevisiae

References / Literature

PMID:26843489 - Mutations in EXOSC2 are associated with a novel syndrome characterised by retinitis pigmentosa, progressive hearing loss, premature ageing, short stature, mild intellectual disability and distinctive gestalt.: Di Donato N et al. J Med Genet 2016 Jun;53(6):419-25
PMID:32012158 - Meiotic gene silencing complex MTREC/NURS recruits the nuclear exosome to YTH-RNA-binding protein Mmi1.: Shichino Y et al. PLoS Genet 2020 Feb;16(2):e1008598
PMID:23163955 - Analysis of stress-induced duplex destabilization (SIDD) properties of replication origins, genes and intergenes in the fission yeast, Schizosaccharomyces pombe.: Yadav MP et al. BMC Res Notes 2012 Nov 19;5:643
PMID:24713849 - Post-transcriptional regulation of meiotic genes by a nuclear RNA silencing complex.: Egan ED et al. RNA 2014 Jun;20(6):867-81
PMID:39705284 - Proteomic and phosphoproteomic analyses reveal that TORC1 is reactivated by pheromone signaling during sexual reproduction in fission yeast.: Bérard M et al. PLoS Biol 2024 Dec 20;22(12):e3002963
PMID:23503588 - The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway.: Malecki M et al. EMBO J 2013 Jul 03;32(13):1842-54
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
GO_REF:0000033 - Annotation inferences using phylogenetic trees
PMID:30321377 - Proteomic profiling and functional characterization of post-translational modifications of the fission yeast RNA exosome.: Telekawa C et al. Nucleic Acids Res 2018 Nov 30;46(21):11169-11183
PMID:25240800 - The RNA exosome promotes transcription termination of backtracked RNA polymerase II.: Lemay JF et al. Nat Struct Mol Biol 2014 Oct;21(10):919-26
PMID:23101633 - Quantitative analysis of fission yeast transcriptomes and proteomes in proliferating and quiescent cells.: Marguerat S et al. Cell 2012 Oct 26;151(3):671-83
PMID:30726745 - Fission Yeast NDR/LATS Kinase Orb6 Regulates Exocytosis via Phosphorylation of the Exocyst Complex.: Tay YD et al. Cell Rep 2019 Feb 05;26(6):1654-1667.e7
PMID:37970674 - SUMOylation regulates Lem2 function in centromere clustering and silencing.: Strachan J et al. J Cell Sci 2023 Dec 01;136(23)
PMID:23697806 - A genome-wide resource of cell cycle and cell shape genes of fission yeast.: Hayles J et al. Open Biol 2013 May 22;3(5):130053
PMID:16823372 - ORFeome cloning and global analysis of protein localization in the fission yeast Schizosaccharomyces pombe.: Matsuyama A et al. Nat Biotechnol 2006 Jul;24(7):841-7
PMID:23755256 - The Sm complex is required for the processing of non-coding RNAs by the exosome.: Coy S et al. PLoS One 2013;8(6):e65606
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
PMID:29906447 - Helicase-Dependent RNA Decay Illuminated by a Cryo-EM Structure of a Human Nuclear RNA Exosome-MTR4 Complex.: Weick EM et al. Cell 2018 Jun 14;173(7):1663-1677.e21
PMID:20473289 - Analysis of a genome-wide set of gene deletions in the fission yeast Schizosaccharomyces pombe.: Kim DU et al. Nat Biotechnol 2010 Jun;28(6):617-623
PMID:24763107 - Absolute proteome and phosphoproteome dynamics during the cell cycle of Schizosaccharomyces pombe (Fission Yeast).: Carpy A et al. Mol Cell Proteomics 2014 Aug;13(8):1925-36
PMID:21511999 - Comparative functional genomics of the fission yeasts.: Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:26771498 - A Proteome-wide Fission Yeast Interactome Reveals Network Evolution Principles from Yeasts to Human.: Vo TV et al. Cell 2016 Jan 14;164(1-2):310-323