Seroatlas · Human Serome Atlas

USP3

Ubiquitin carboxyl-terminal hydrolase 3

Also known as: UBP3_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession
Q9Y6I4
Gene
USP3
Ensembl
ENSG00000140455
Chromosome
15
Canonical length
520 aa
Protein class
Enzymes, Metabolic proteins, Predicted intracellular proteins
Subcellular location
Nucleoplasm,Midbody ring
Secretome location
Intracellular and membrane

OverviewNCBI Gene

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]

Canonical amino-acid sequenceUniProt

520 residues, UniProt reviewed canonical sequence.

>Q9Y6I4|USP3
     1  MECPHLSSSV CIAPDSAKFP NGSPSSWCCS VCRSNKSPWV CLTCSSVHCG RYVNGHAKKH
    61  YEDAQVPLTN HKKSEKQDKV QHTVCMDCSS YSTYCYRCDD FVVNDTKLGL VQKVREHLQN
   121  LENSAFTADR HKKRKLLENS TLNSKLLKVN GSTTAICATG LRNLGNTCFM NAILQSLSNI
   181  EQFCCYFKEL PAVELRNGKT AGRRTYHTRS QGDNNVSLVE EFRKTLCALW QGSQTAFSPE
   241  SLFYVVWKIM PNFRGYQQQD AHEFMRYLLD HLHLELQGGF NGVSRSAILQ ENSTLSASNK
   301  CCINGASTVV TAIFGGILQN EVNCLICGTE SRKFDPFLDL SLDIPSQFRS KRSKNQENGP
   361  VCSLRDCLRS FTDLEELDET ELYMCHKCKK KQKSTKKFWI QKLPKVLCLH LKRFHWTAYL
   421  RNKVDTYVEF PLRGLDMKCY LLEPENSGPE SCLYDLAAVV VHHGSGVGSG HYTAYATHEG
   481  RWFHFNDSTV TLTDEETVVK AKAYILFYVE HQAKAGSDKL

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against USP3 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability
Intracellular
Secreted
No
Transmembrane segments
0
Mean surface accessibility (rSASA)
0.33
Highest tissue expression
24 nTPM

Expression across tissuesHPA

Tissue

  • cerebellum: 24 nTPM
  • bone marrow: 20 nTPM
  • pancreas: 9.5 nTPM
  • spleen: 9.4 nTPM
  • stomach: 8.9 nTPM
  • skin: 8.1 nTPM

Single-cell type

  • neutrophils: 1,742 nCPM
  • neutrophil progenitors: 629 nCPM
  • endometrial glandular cells: 534 nCPM
  • monocyte progenitors: 485 nCPM
  • monocytes: 458 nCPM
  • pancreatic acinar cells: 291 nCPM

Immune cell

  • neutrophil: 170 nTPM
  • basophil: 121 nTPM
  • classical monocyte: 85 nTPM
  • intermediate monocyte: 66 nTPM
  • non-classical monocyte: 66 nTPM
  • myeloid DC: 60 nTPM

Brain region

  • cerebellum: 89 nTPM
  • choroid plexus: 46 nTPM
  • thalamus: 34 nTPM
  • pons: 30 nTPM
  • medulla oblongata: 29 nTPM
  • white matter: 29 nTPM

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance)
0.16
gnomAD pLI
1
gnomAD missense Z
2.11
DepMap mean gene effect
-0.03
DepMap dependency class
selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads USP3 as an antibody target. Whether an autoantibody or antibody against USP3 could matter depends on whether native USP3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

USP3 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label USP3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/USP3. Study-independent annotations aggregated from UniProt, Human Protein Atlas, PubMed, IEDB, Pfam, InterPro, Gene Ontology, AlphaFold, gnomAD, DepMap, ClinVar, TCGA. Catalog release seroatlas-reviewed-human-uniprot-20260313.

Seroatlas is the reference for exploring autoantibody and antibody serology at the human-protein level: the autoreactome and human serome, multiplex serology (HuProt, HuScan, VirScan, PhIP-Seq).

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