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protein coding gene - csl4 (SPCC1840.11) - exosome subunit Csl4

Gene summary

Standard name
csl4
Systematic ID
SPCC1840.11
Product
exosome subunit Csl4
Organism
Schizosaccharomyces pombe (fission yeast)
Synonyms
SPCC965.01
UniProt ID
O59821
ORFeome ID
05/05E11
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome III: 2279268..2280286 forward strand

Annotation

Disease association

MONDO:0030261 - pontocerebellar hypoplasia, type 1F

References:

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:0071028 - nuclear mRNA surveillance

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GO:0071042 - nuclear polyadenylation-dependent mRNA catabolic process

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GO:0071035 - nuclear polyadenylation-dependent rRNA catabolic process

References:

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

References:

GO:0071038 - TRAMP-dependent tRNA surveillance pathway

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GO cellular component

GO:0000785 - chromatin

References:

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

References:

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

References:

MOD:00048 - O4'-phospho-L-tyrosine

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Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000012 - RNA level decreased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

References:

Single locus phenotype

FYPO:0002060 - viable vegetative cell population

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Genotypes:

FYPO:0002177 - viable vegetative cell with normal cell morphology

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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
PF10447EXOSC1EXOSC1_CPfam
cd05791S1_CSL4CDD
PS50126S1S1_domainPROSITE profiles
SM00316S1S1_domainSMART
G3DSA:2.40.50.140:FF:000198CATH-FunFam
G3DSA:2.40.50.100CATH-Gene3D
G3DSA:2.40.50.140NA-bd_OB-foldCATH-Gene3D
SSF50249NA-bd_OB-foldSUPERFAMILY
PTHR12686Csl4PANTHER

Orthologs

References / Literature

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: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
GO_REF:0000002 - Comments
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
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
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: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: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
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: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: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:31626996 - Multiplexed proteome profiling of carbon source perturbations in two yeast species with SL-SP3-TMT.
Paulo JA et al. J Proteomics 2020 Jan 06;210:103531
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: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: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