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protein coding gene - rrp40 (SPAC22A12.12c) - exosome subunit Rrp40

Gene summary

Standard name
rrp40
Systematic ID
SPAC22A12.12c
Product
exosome subunit Rrp40
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
O13903
ORFeome ID
08/08E12
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome I: 1178856..1179940 reverse strand

Annotation

Disease association

MONDO:0020135 - pontocerebellar hypoplasia

References:

MONDO:0016396 - pontocerebellar hypoplasia type 1

References:

MONDO:0013853 - pontocerebellar hypoplasia type 1B

References:

GO biological process

GO:0071034 - CUT catabolic process

References:

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

References:

GO:0071028 - nuclear mRNA surveillance

References:

GO:0071042 - nuclear polyadenylation-dependent mRNA catabolic process

References:

GO:0071035 - nuclear polyadenylation-dependent rRNA catabolic process

References:

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

References:

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

References:

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

References:

GO:0071038 - TRAMP-dependent tRNA surveillance pathway

References:

GO:0034475 - U4 snRNA 3'-end processing

References:

GO cellular component

GO:0000177 - cytoplasmic exosome (RNase complex)

References:

GO:0000178 - exosome (RNase complex)

References:

GO:0000176 - nuclear exosome (RNase complex)

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GO molecular function

GO:0003723 - RNA binding

References:

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

References:

Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0000059 - abnormal mitotic cell cycle

References:

Genotypes:

FYPO:0002379 - inviable after spore germination, without cell division, with elongated germ tube

References:

Genotypes:

FYPO:0000310 - inviable after spore germination, without cell division, with normal germ tube morphology

References:

Genotypes:

FYPO:0002061 - inviable vegetative cell population

References:

Genotypes:

Taxonomic conservation

PBO:0011072 - conserved in archaea

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
PF15985KH_6KH_dom_type_1Pfam
PF18311Rrp40_NRrp40_N_eukPfam
PF21262RRP40_S1Pfam
cd05790S1_Rrp40Rrp40_S1CDD
cd22526KH-I_Rrp40RRP40_KH-ICDD
G3DSA:2.40.50.140:FF:000112CATH-FunFam
G3DSA:3.30.1370.10:FF:000038CATH-FunFam
G3DSA:2.40.50.100CATH-Gene3D
G3DSA:2.40.50.140NA-bd_OB-foldCATH-Gene3D
G3DSA:3.30.1370.10KH_dom_type_1_sfCATH-Gene3D
SSF50249NA-bd_OB-foldSUPERFAMILY
SSF54791KH_dom_type_1_sfSUPERFAMILY
PTHR21321Exosome_RNA_bind1/RRP40/RRP4PANTHER

Orthologs

References / Literature

PMID:29727687 - Variants in EXOSC9 Disrupt the RNA Exosome and Result in Cerebellar Atrophy with Spinal Motor Neuronopathy.
Burns DT et al. Am J Hum Genet 2018 May 03;102(5):858-873
PMID:16537923 - Sterol regulatory element binding protein is a principal regulator of anaerobic gene expression in fission yeast.
Todd BL et al. Mol Cell Biol 2006 Apr;26(7):2817-31
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: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
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:22907753 - Posttranscriptional regulation of cell-cell interaction protein-encoding transcripts by Zfs1p in Schizosaccharomyces pombe.
Wells ML et al. Mol Cell Biol 2012 Oct;32(20):4206-14
PMID:39367033 - Quantitative proteomics and phosphoproteomics profiling of meiotic divisions in the fission yeast Schizosaccharomyces pombe.
Sivakova B et al. Sci Rep 2024 Oct 04;14(1):23105
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:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
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
PB_REF:0000003 - Disease Association Curation
PB_REF:0000006 - Disease associations from Monarch via human-pombe orthologs
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: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: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: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
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: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: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