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protein coding gene - rrp41 (SPAC3G9.10c) - exosome subunit Rrp41

Gene summary

Standard name
rrp41
Systematic ID
SPAC3G9.10c
Product
exosome subunit Rrp41
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
O42872
ORFeome ID
12/12A06
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 3163127..3164354 forward strand

Annotation

GO biological process

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:0070651 - nonfunctional rRNA decay

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GO:0071031 - nuclear mRNA surveillance of mRNA 3'-end processing

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GO:0071042 - nuclear polyadenylation-dependent mRNA catabolic process

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GO:0071035 - nuclear polyadenylation-dependent rRNA catabolic process

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GO:0071027 - nuclear RNA surveillance

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

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

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

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GO:0030847 - termination of RNA polymerase II transcription, exosome-dependent

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GO:0071038 - TRAMP-dependent tRNA surveillance pathway

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GO:0034475 - U4 snRNA 3'-end processing

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GO cellular component

GO:0000785 - chromatin

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GO:0000177 - cytoplasmic exosome (RNase complex)

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GO:0005829 - cytosol

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GO:0000178 - exosome (RNase complex)

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GO:0000176 - nuclear exosome (RNase complex)

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GO:0005730 - nucleolus

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GO:0005634 - nucleus

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GO molecular function

GO:0003723 - RNA binding

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Modification

MOD:00046 - O-phospho-L-serine

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Qualitative gene expression

PomGeneEx:0000012 - RNA level decreased

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Quantitative gene expression

PBO:0006310 - protein level

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PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0004811 - abnormal termination of RNA polymerase II transcription

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Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0003700 - increased snoRNA primary transcript level

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Genotypes:

FYPO:0003049 - increased transcriptional readthrough

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Genotypes:

FYPO:0000311 - inviable after spore germination with normal, unseptated germ tube morphology

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Genotypes:

FYPO:0002151 - inviable spore

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Genotypes:

FYPO:0002061 - inviable vegetative cell population

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Genotypes:

FYPO:0001234 - slow vegetative cell population growth

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Genotypes:

Taxonomic conservation

PBO:0011065 - conserved in eukaryotes

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

IDNameInterPro nameDB name
PF01138RNase_PHExoRNase_PH_dom1PFAM
PF03725RNase_PH_CExoRNase_PH_dom2PFAM
cd11370RNase_PH_RRP41CDD
G3DSA:3.30.230.70:FF:000004FUNFAM
SSF55666Ribonuclease PH domain 2-likeExoRNase_PH_dom2_sfSUPERFAMILY
SSF54211Ribosomal protein S5 domain 2-likeRibosomal_Su5_D2-typ_SFSUPERFAMILY
G3DSA:3.30.230.70PNPase/RNase_PH_dom_sfGENE3D
PTHR11953EXOSOME COMPLEX COMPONENTRNase_PHPANTHER

Orthologs

References / Literature

PMID:33313903 - Ribosome profiling reveals ribosome stalling on tryptophan codons and ribosome queuing upon oxidative stress in fission yeast.
Rubio A et al. Nucleic Acids Res 2021 Jan 11;49(1):383-399
GO_REF:0000033 - Annotation inferences using phylogenetic trees
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: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:11751918 - The fission yeast ES2 homologue, Bis1, interacts with the Ish1 stress-responsive nuclear envelope protein.
Taricani L et al. J Biol Chem 2002 Mar 22;277(12):10562-72
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: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:32101745 - Dense Transposon Integration Reveals Essential Cleavage and Polyadenylation Factors Promote Heterochromatin Formation.
Lee SY et al. Cell Rep 2020 Feb 25;30(8):2686-2698.e8
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
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: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:23503588 - The exoribonuclease Dis3L2 defines a novel eukaryotic RNA degradation pathway.
Malecki M et al. EMBO J 2013 Jul 03;32(13):1842-54
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:25720772 - Quantitative phosphoproteomics reveals pathways for coordination of cell growth and division by the conserved fission yeast kinase pom1.
Kettenbach AN et al. Mol Cell Proteomics 2015 May;14(5):1275-87
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
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: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