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Guidelines

MIRAGE

mRNA-binding ubiquitin-specific protease UBP3

Summary

Gene Symbol

UBP3

Organism

Saccharomyces cerevisiae S288C

External Links

NCBI Gene

856895

KEGG Gene ID

PubChem

856895

Alliance of Genome Resources

SGD:S000000953

Annotation

Keyword

3D-structure
Reference proteome
Thiol protease
Ubl conjugation pathway

Proteins

Displaying 1 entry
UniProt	Protein Name
Q01477	Deubiquitinating enzyme 3 Ubiquitin thioesterase 3 Ubiquitin-specific-processing protease 3

Annotation information from UniProt.

Gene Ontology (GO)

Displaying entries **1 - 5** of 16 in total

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GO Term	Evidence Code	PMID
proteolysis
protein deubiquitination	IDA
protein deubiquitination	IMP
protein deubiquitination	IEA
regulation of protein stability	IBA

GO Hierarchy

biological process

cellular process [inference]

metabolic process [inference]

catabolic process [inference]

autophagy [inference]

macroautophagy [inference]

ribophagy

macromolecule metabolic process [inference]

protein metabolic process [inference]

proteolysis

protein modification process [inference]

post-translational protein modification [inference]

protein modification by small protein conjugation or removal [inference]

protein modification by small protein removal [inference]

protein deubiquitination

macromolecule modification [inference]

protein modification process [inference]

post-translational protein modification [inference]

protein modification by small protein conjugation or removal [inference]

protein modification by small protein removal [inference]

protein deubiquitination

primary metabolic process [inference]

protein metabolic process [inference]

proteolysis

protein modification process [inference]

post-translational protein modification [inference]

protein modification by small protein conjugation or removal [inference]

protein modification by small protein removal [inference]

protein deubiquitination

maintenance of location in cell [inference]

maintenance of protein location in cell [inference]

protein retention in Golgi apparatus

process utilizing autophagic mechanism [inference]

autophagy [inference]

macroautophagy [inference]

ribophagy

cellular component organization or biogenesis [inference]

cellular component organization [inference]

organelle organization [inference]

organelle assembly [inference]

membraneless organelle assembly [inference]

stress granule assembly

cellular component assembly [inference]

organelle assembly [inference]

membraneless organelle assembly [inference]

stress granule assembly

localization [inference]

maintenance of location [inference]

maintenance of protein location [inference]

maintenance of protein location in cell [inference]

protein retention in Golgi apparatus

maintenance of location in cell [inference]

maintenance of protein location in cell [inference]

protein retention in Golgi apparatus

biological regulation [inference]

regulation of biological process [inference]

regulation of localization [inference]

regulation of transport [inference]

regulation of intracellular transport [inference]

regulation of ER to Golgi vesicle-mediated transport

regulation of vesicle-mediated transport [inference]

regulation of cellular localization [inference]

regulation of intracellular transport [inference]

regulation of ER to Golgi vesicle-mediated transport

negative regulation of biological process [inference]

negative regulation of cellular process [inference]

negative regulation of metabolic process [inference]

negative regulation of catabolic process [inference]

negative regulation of autophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

regulation of response to stimulus [inference]

regulation of response to stress [inference]

regulation of response to osmotic stress

regulation of cellular process [inference]

regulation of metabolic process [inference]

negative regulation of metabolic process [inference]

negative regulation of catabolic process [inference]

negative regulation of autophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

regulation of catabolic process [inference]

negative regulation of catabolic process [inference]

negative regulation of autophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

regulation of autophagy [inference]

negative regulation of autophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

regulation of macroautophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

regulation of mitophagy [inference]

negative regulation of mitophagy

regulation of autophagy of mitochondrion [inference]

regulation of mitophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

negative regulation of cellular process [inference]

negative regulation of metabolic process [inference]

negative regulation of catabolic process [inference]

negative regulation of autophagy [inference]

negative regulation of macroautophagy [inference]

negative regulation of mitophagy

negative regulation of autophagy of mitochondrion [inference]

negative regulation of mitophagy

regulation of cellular localization [inference]

regulation of intracellular transport [inference]

regulation of ER to Golgi vesicle-mediated transport

regulation of vesicle-mediated transport [inference]

regulation of biological quality [inference]

regulation of protein stability

Displaying entries **1 - 5** of 7 in total

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GO Term	Evidence Code	PMID
nucleus	IBA
cytoplasm	IDA
mitochondrion	IDA
cytosol	IDA
cytosol	IBA

GO Hierarchy

cellular component

protein-containing complex [inference]

catalytic complex [inference]

peptidase complex [inference]

Ubp3-Bre5 deubiquitination complex

cellular anatomical structure [inference]

organelle [inference]

membrane-bounded organelle [inference]

intracellular membrane-bounded organelle [inference]

intracellular organelle [inference]

intracellular membrane-bounded organelle [inference]

Displaying entries **1 - 5** of 8 in total

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GO Term	Evidence Code	PMID
mRNA binding	IDA
mRNA binding	HDA
cysteine-type deubiquitinase activity	EXP
cysteine-type deubiquitinase activity	IDA
cysteine-type deubiquitinase activity	IMP

GO Hierarchy

molecular function

catalytic activity [inference]

hydrolase activity [inference]

peptidase activity [inference]

cysteine-type peptidase activity [inference]

cysteine-type deubiquitinase activity

ubiquitin-like protein peptidase activity [inference]

deubiquitinase activity [inference]

cysteine-type deubiquitinase activity

catalytic activity, acting on a protein [inference]

peptidase activity [inference]

cysteine-type peptidase activity [inference]

cysteine-type deubiquitinase activity

ubiquitin-like protein peptidase activity [inference]

deubiquitinase activity [inference]

cysteine-type deubiquitinase activity

binding [inference]

nucleic acid binding [inference]

RNA binding [inference]

mRNA binding

protein binding

Gene Ontology information from NCBI Gene and UniProt.

Alliance of Genome Resources

Expression

Displaying **all 3** entries
Location	References
cytosol	PMID:26928762
Ubp3-Bre5 deubiquitination complex	PMID:12778054
cytoplasm	PMID:23222640

Ortholog

Displaying **all 2** entries
Species	Gene ID	Alliance of Genome Resources
Mus musculus	22224	MGI:894652
Homo sapiens	9100	HGNC:12608

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Supported by JST NBDC Grant Number JPMJND2204

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Last updated: April 6, 2026