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protein coding gene - ubp3 (SPBP8B7.21) - ubiquitin C-terminal hydrolase Ubp3

Gene summary

Standard name
ubp3
Systematic ID
SPBP8B7.21
Product
ubiquitin C-terminal hydrolase Ubp3
Organism
Schizosaccharomyces pombe (fission yeast)
UniProt ID
O94269
ORFeome ID
25/25D05
Characterisation status
biological role published
Feature type
mRNA gene
Genomic location
chromosome II: 3677649..3679661 forward strand

Annotation

GO biological process

GO:0071629 - cytoplasm protein quality control by the ubiquitin-proteasome system

References:

GO:2000156 - regulation of retrograde vesicle-mediated transport, Golgi to ER

References:

GO cellular component

GO:0005737 - cytoplasm

References:

GO:0010494 - cytoplasmic stress granule

References:

GO:0005829 - cytosol

References:

GO:0005634 - nucleus

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GO molecular function

GO:0004843 - cysteine-type deubiquitinase activity

References:

GO:0140492 - metal-dependent deubiquitinase activity

References:

Modification

MOD:00046 - O-phospho-L-serine

References:

Multi-locus phenotype

FYPO:0002350 - normal stress granule assembly during vegetative growth

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

Qualitative gene expression

PomGeneEx:0000019 - protein level decreased

References:

PomGeneEx:0000026 - ribosomal density increased

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PomGeneEx:0000012 - RNA level decreased

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Quantitative gene expression

PBO:0006310 - protein level

References:

PBO:0011963 - RNA level

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Single locus phenotype

FYPO:0007562 - decreased cell population growth on serine nitrogen source

References:

Genotypes:

FYPO:0003412 - decreased chromatin silencing at centromere outer repeat

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Genotypes:

FYPO:0003151 - decreased protein level during cellular response to heat

References:

Genotypes:

FYPO:0004167 - increased cell population growth on glycerol carbon source

References:

Genotypes:

FYPO:0008413 - increased establishment of chromatin silencing at centromere outer repeat region

References:

Genotypes:

FYPO:0001309 - increased viability in stationary phase

References:

Genotypes:

FYPO:0001023 - normal growth on cisplatin

References:

Genotypes:

FYPO:0004744 - normal heterochromatin maintenance involved in chromatin silencing at centromere outer repeat

References:

Genotypes:

FYPO:0007323 - normal stress granule assembly during cellular response to heat

References:

Genotypes:

FYPO:0002350 - normal stress granule assembly during vegetative growth

References:

Genotypes:

FYPO:0001357 - normal vegetative cell population growth

References:

Genotypes:

FYPO:0009041 - resistance to 2,2′-dipyridyl

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Genotypes:

FYPO:0002693 - resistance to diamide

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Genotypes:

FYPO:0009038 - resistance to egtazic acid

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Genotypes:

FYPO:0009070 - resistance to itraconazole

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Genotypes:

FYPO:0001583 - resistance to lithium

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Genotypes:

FYPO:0009083 - resistance to lithium chloride and methyl methanesulfonate

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Genotypes:

FYPO:0009085 - resistance to lithium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0009087 - resistance to magnesium chloride and sodium dodecyl sulfate

References:

Genotypes:

FYPO:0005253 - resistance to tamoxifen

References:

Genotypes:

FYPO:0003383 - resistance to tert-butyl hydroperoxide

References:

Genotypes:

FYPO:0001034 - resistance to tunicamycin

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Genotypes:

FYPO:0000830 - resistance to vanadate

References:

Genotypes:

FYPO:0001501 - sensitive to brefeldin A

References:

Genotypes:

FYPO:0000097 - sensitive to caffeine during vegetative growth

References:

Genotypes:

FYPO:0000104 - sensitive to cycloheximide

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Genotypes:

FYPO:0000088 - sensitive to hydroxyurea

References:

Genotypes:

FYPO:0001214 - sensitive to potassium chloride

References:

Genotypes:

FYPO:0002701 - sensitive to torin1

References:

Genotypes:

FYPO:0002060 - viable vegetative cell population

References:

Genotypes:

FYPO:0002177 - viable vegetative cell with normal cell morphology

References:

Genotypes:

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

IDNameInterPro nameDB name
PF00443UCHPeptidase_C19_UCHPFAM
cd02257Peptidase_C19CDD
PS00972USP_1USP_CSPROSITE_PATTERNS
PS00973USP_2USP_CSPROSITE_PATTERNS
PS50235USP_3USPPROSITE_PROFILES
G3DSA:3.90.70.10:FF:000092FUNFAM
SSF54001Cysteine proteinasesPapain-like_cys_pep_sfSUPERFAMILY
G3DSA:3.90.70.10Cysteine proteinasesGENE3D
PTHR24006UBIQUITIN CARBOXYL-TERMINAL HYDROLASEPeptidase_C19PANTHER
mobidb-lite-Disorderdisorder_predictionMOBIDB-Disorder

Orthologs

References / Literature

PMID:21182284 - Survey of the phosphorylation status of the Schizosaccharomyces pombe deubiquitinating enzyme (DUB) family.
McLean JR et al. J Proteome Res 2011 Mar 04;10(3):1208-15
PMID:22328580 - Analysis of stress granule assembly in Schizosaccharomyces pombe.
Wang CY et al. RNA 2012 Apr;18(4):694-703
PMID:24497846 - A chaperone-assisted degradation pathway targets kinetochore proteins to ensure genome stability.
Kriegenburg F et al. PLoS Genet 2014 Jan;10(1):e1004140
PMID:21247416 - Ubiquitin-proteasome genes as targets for modulation of cisplatin sensitivity in fission yeast.
Gatti L et al. BMC Genomics 2011 Jan 19;12:44
PMID:22681890 - Hierarchical modularity and the evolution of genetic interactomes across species.
Ryan CJ et al. Mol Cell 2012 Jun 08;46(5):691-704
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:26628015 - Characterization of Tamoxifen as an Antifungal Agent Using the Yeast Schizosaccharomyces Pombe Model Organism.
Zhang X et al. Kobe J Med Sci 2015 Oct 09;61(2):E54-63
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:18931302 - Significant conservation of synthetic lethal genetic interaction networks between distantly related eukaryotes.
Dixon SJ et al. Proc Natl Acad Sci U S A 2008 Oct 28;105(43):16653-8
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
PMID:34250083 - Barcode sequencing and a high-throughput assay for chronological lifespan uncover ageing-associated genes in fission yeast.
Romila CA et al. Microb Cell 2021 Jul 05;8(7):146-160
PMID:37787768 - Broad functional profiling of fission yeast proteins using phenomics and machine learning.
Rodríguez-López M et al. Elife 2023 Oct 03;12
PMID:24957674 - Yeast X-chromosome-associated protein 5 (Xap5) functions with H2A.Z to suppress aberrant transcripts.
Anver S et al. EMBO Rep 2014 Aug;15(8):894-902
PMID:33823663 - A TOR (target of rapamycin) and nutritional phosphoproteome of fission yeast reveals novel targets in networks conserved in humans.
Halova L et al. Open Biol 2021 Apr;11(4):200405
PMID:21892171 - Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin.
Reyes-Turcu FE et al. Nat Struct Mol Biol 2011 Sep 04;18(10):1132-8
PMID:18818364 - Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast.
Roguev A et al. Science 2008 Oct 17;322(5900):405-10
GO_REF:0000024 - Manual transfer of experimentally-verified manual GO annotation data to orthologs by curator judgment of sequence similarity.
PMID:28765280 - The exocyst subunit Sec3 is regulated by a protein quality control pathway.
Kampmeyer C et al. J Biol Chem 2017 Sep 15;292(37):15240-15253
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:20838651 - A global census of fission yeast deubiquitinating enzyme localization and interaction networks reveals distinct compartmentalization profiles and overlapping functions in endocytosis and polarity.
Kouranti I et al. PLoS Biol 2010 Sep 07;8(9)
PMID:35820914 - Antagonistic effects of mitochondrial matrix and intermembrane space proteases on yeast aging.
Vega M et al. BMC Biol 2022 Jul 12;20(1):160
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:27984744 - Survival in Quiescence Requires the Euchromatic Deployment of Clr4/SUV39H by Argonaute-Associated Small RNAs.
Joh RI et al. Mol Cell 2016 Dec 15;64(6):1088-1101
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:21712547 - Mitotic substrates of the kinase aurora with roles in chromatin regulation identified through quantitative phosphoproteomics of fission yeast.
Koch A et al. Sci Signal 2011 Jun 28;4(179):rs6
PMID:40063661 - Fission yeast Caprin protein is required for efficient heterochromatin establishment.
Zhang H et al. PLoS Genet 2025 Mar 10;21(3):e1011620
PMID:19547744 - Evolution of phosphoregulation: comparison of phosphorylation patterns across yeast species.
Beltrao P et al. PLoS Biol 2009 Jun 16;7(6):e1000134
PMID:21511999 - Comparative functional genomics of the fission yeasts.
Rhind N et al. Science 2011 May 20;332(6032):930-6
PMID:28218250 - Chromatin remodeller Fun30 Fft3 induces nucleosome disassembly to facilitate RNA polymerase II elongation.
Lee J et al. Nat Commun 2017 Feb 20;8:14527
PMID:29996109 - Quantitative Phosphoproteomics Reveals the Signaling Dynamics of Cell-Cycle Kinases in the Fission Yeast Schizosaccharomyces pombe.
Swaffer MP et al. Cell Rep 2018 Jul 10;24(2):503-514
PMID:32071154 - Fission Yeast Puf2, a Pumilio and FBF Family RNA-Binding Protein, Links Stress Granules to Processing Bodies.
Hsiao WY et al. Mol Cell Biol 2020 Apr 13;40(9)
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:24463365 - Systematic screen for mutants resistant to TORC1 inhibition in fission yeast reveals genes involved in cellular ageing and growth.
Rallis C et al. Biol Open 2014 Feb 15;3(2):161-71
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