Human_Genes_Functions
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Prototype stage

Gene detail

Read-only gene view with summary, GO, UniProt, NCBI, and representative sequence links.

GRCh38.p14 + GENCODE Release 50local-onlyPDO SQLite primaryread-only query modesqlite3 fallback available

Gene detail

USP3

USP3

protein_coding 15 63,504,501 - 63,594,640 PDO SQLite primary read-only query mode
Overview Summary GO UniProt Representative Transcripts FASTA ClinVar disease associations

Overview

Gene ID
ENSG00000140455
Gene type
protein_coding
Chromosome
15
Coordinates
63,504,501 - 63,594,640
Strand
+
Status
not available
NCBI summary UniProt GO Transcript FASTA Protein FASTA

Aliases

9960 CCDS32265 CCDS58370 ENST00000380324.8 NM_001256702 NM_006537.4 Q9Y6I4 ubiquitin specific protease 3

Summary

GENCODE gene_type=protein_coding; HGNC symbol=USP3; HGNC name=ubiquitin specific peptidase 3; alias_count=8; RefSeq=NM_001256702; UniProt=Q9Y6I4; MANE Select=ENST00000380324.8,NM_006537.4

Source: GENCODE + HGNC complete set

9960 • protein-coding

Alliance of Genome Resources Enables deubiquitinase activity and histone binding activity. Involved in DNA repair and DNA repair-dependent chromatin remodeling. Located in several cellular components, including Flemming body; cytoplasmic ribonucleoprotein granule; and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]

NCBI Gene

UniProt

Q9Y6I4 • reviewed

Deubiquitinase that plays a role in several cellular processes including transcriptional regulation, cell cycle progression or innate immunity. In response to DNA damage, deubiquitinates monoubiquitinated target proteins such as histone H2A and H2AX and thereby counteracts RNF168- and RNF8-mediated ubiquitination. In turn, participates in the recruitment of DNA damage repair factors to DNA break sites (PubMed:24196443). Required for proper progression through S phase and subsequent mitotic entry (PubMed:17980597). Acts as a positive regulator of TP53 by deubiquitinating and stabilizing it to promote normal cell proliferation and transformation (PubMed:28807825). Participates in establishing tolerance innate immune memory through non-transcriptional feedback. Mechanistically, negatively regulates TLR-induced NF-kappa-B signaling by targeting and removing the 'Lys-63'-linked polyubiquitin chains on MYD88 (PubMed:37971847). Negatively regulates the activation of type I interferon signaling by mediating 'Lys-63'-linked polyubiquitin chains on RIGI and IFIH1 (PubMed:24366338). Also deubiquitinates ASC/PYCARD, the central adapter mediating the assembly and activation of most inflammasomes, and thereby promotes inflammasome activation (PubMed:36050480)

Ubiquitin carboxyl-terminal hydrolase 3 · Nucleus; Cytoplasm · EC 3.4.19.12

Q9Y6I4 • reviewed

Deubiquitinase that plays a role in several cellular processes including transcriptional regulation, cell cycle progression or innate immunity. In response to DNA damage, deubiquitinates monoubiquitinated target proteins such as histone H2A and H2AX and thereby counteracts RNF168- and RNF8-mediated ubiquitination. In turn, participates in the recruitment of DNA damage repair factors to DNA break sites (PubMed:24196443). Required for proper progression through S phase and subsequent mitotic entry (PubMed:17980597). Acts as a positive regulator of TP53 by deubiquitinating and stabilizing it to promote normal cell proliferation and transformation (PubMed:28807825). Participates in establishing tolerance innate immune memory through non-transcriptional feedback. Mechanistically, negatively regulates TLR-induced NF-kappa-B signaling by targeting and removing the 'Lys-63'-linked polyubiquitin chains on MYD88 (PubMed:37971847). Negatively regulates the activation of type I interferon signaling by mediating 'Lys-63'-linked polyubiquitin chains on RIGI and IFIH1 (PubMed:24366338). Also deubiquitinates ASC/PYCARD, the central adapter mediating the assembly and activation of most inflammasomes, and thereby promotes inflammasome activation (PubMed:36050480)

Ubiquitin carboxyl-terminal hydrolase 3 · Nucleus; Cytoplasm · EC 3.4.19.12

GO annotations

Biological process
  • GO:0006281 DNA repair (IMP)
  • GO:0140861 DNA repair-dependent chromatin remodeling (IDA)
  • GO:0016579 protein deubiquitination (IEA)
Cellular component
  • GO:0000785 chromatin (IDA)
  • GO:0005737 cytoplasm (IEA)
  • GO:0005737 cytoplasm (EXP)
  • GO:0005654 nucleoplasm (IDA)
  • GO:0005654 nucleoplasm (TAS)
  • GO:0005634 nucleus (IEA)
  • GO:0005634 nucleus (EXP)
  • GO:0005634 nucleus (EXP)
  • GO:0005634 nucleus (EXP)
  • GO:0005634 nucleus (IBA)
Molecular function
  • GO:0004843 cysteine-type deubiquitinase activity (IEA)
  • GO:0004843 cysteine-type deubiquitinase activity (IEA)
  • GO:0004843 cysteine-type deubiquitinase activity (IEA)
  • GO:0004843 cysteine-type deubiquitinase activity (TAS)
  • GO:0004843 cysteine-type deubiquitinase activity (IMP)
  • GO:0004843 cysteine-type deubiquitinase activity (EXP)
  • GO:0004843 cysteine-type deubiquitinase activity (EXP)
  • GO:0004843 cysteine-type deubiquitinase activity (EXP)
  • GO:0004843 cysteine-type deubiquitinase activity (EXP)
  • GO:0140950 histone H2A deubiquitinase activity (IMP)

+ 3 more

Representative

Representative transcript
ENST00000380324
Representative protein
ENSP00000369681.3
Representative type
CCDS
Candidate count
6

GENCODE Release 50 annotation GTF · transcript.tag=CCDS; transcript_support_level=1

Transcript FASTA Protein FASTA

Transcripts

Transcript ID Name Type Status Protein Location
ENST00000540797 USP3-204 protein_coding not available ENSP00000445828.1 15:63,504,501 - 63,594,640 +
ENST00000875483 USP3-222 protein_coding not available ENSP00000545542.1 15:63,504,501 - 63,594,640 +
ENST00000875484 USP3-223 protein_coding not available ENSP00000545543.1 15:63,504,501 - 63,594,640 +
ENST00000969958 USP3-224 protein_coding not available ENSP00000640017.1 15:63,504,501 - 63,594,640 +
ENST00000969959 USP3-225 protein_coding not available ENSP00000640018.1 15:63,504,501 - 63,594,640 +
ENST00000969960 USP3-226 protein_coding not available ENSP00000640019.1 15:63,504,501 - 63,594,640 +
ENST00000969961 USP3-227 protein_coding not available ENSP00000640020.1 15:63,504,501 - 63,594,640 +
ENST00000969962 USP3-228 protein_coding not available ENSP00000640021.1 15:63,504,501 - 63,594,640 +
ENST00001132619 USP3-235 protein_coding not available ENSP00000811101.1 15:63,504,501 - 63,594,640 +
ENST00001047463 USP3-230 nonsense_mediated_decay not available ENSP00000717280.1 15:63,504,523 - 63,591,467 +
ENST00001000189 USP3-229 nonsense_mediated_decay not available ENSP00000670006.1 15:63,504,565 - 63,591,464 +
ENST00001047464 USP3-231 nonsense_mediated_decay not available ENSP00000717281.1 15:63,504,578 - 63,591,462 +
ENST00001047465 USP3-232 nonsense_mediated_decay not available ENSP00000717282.1 15:63,504,592 - 63,591,463 +
ENST00000380324 USP3-202 protein_coding not available ENSP00000369681.3 15:63,504,593 - 63,594,633 +
ENST00000561442 USP3-221 protein_coding not available ENSP00000453688.1 15:63,504,594 - 63,553,733 +
ENST00000560070 USP3-217 protein_coding not available ENSP00000453194.1 15:63,504,595 - 63,558,187 +
ENST00001047466 USP3-233 nonsense_mediated_decay not available ENSP00000717283.1 15:63,504,601 - 63,591,467 +
ENST00000557884 USP3-205 nonsense_mediated_decay not available ENSP00000454043.1 15:63,504,612 - 63,559,884 +
ENST00001066381 USP3-234 nonsense_mediated_decay not available ENSP00000736187.1 15:63,504,615 - 63,591,474 +
ENST00000558157 USP3-206 nonsense_mediated_decay not available ENSP00000452929.1 15:63,504,635 - 63,591,444 +

FASTA

FASTA output is generated by backend query; the raw FASTA path is not exposed.

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ClinVar disease associations

ClinVar disease associations: 0

ClinVar gene-disease tables are missing. Build the candidate database first.