Seroatlas · Human Serome Atlas

USP39

Ubiquitin carboxyl-terminal hydrolase 39

Also known as: CGI-21, SAD1, SNRNP65, UBP39_HUMAN

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

Protein identityUniProt · HPA

UniProt accession
Q53GS9
Gene
USP39
Ensembl
ENSG00000168883
Chromosome
2
Canonical length
565 aa
Protein class
Enzymes, Predicted intracellular proteins
Subcellular location
Nucleoplasm

OverviewNCBI Gene

Predicted to enable cysteine-type deubiquitinase activity and zinc ion binding activity. Involved in spliceosomal complex assembly. Located in nucleoplasm. Part of U4/U6 x U5 tri-snRNP complex. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

565 residues, UniProt reviewed canonical sequence.

>Q53GS9|USP39
     1  MSGRSKRESR GSTRGKRESE SRGSSGRVKR ERDREREPEA ASSRGSPVRV KREFEPASAR
    61  EAPASVVPFV RVKREREVDE DSEPEREVRA KNGRVDSEDR RSRHCPYLDT INRSVLDFDF
   121  EKLCSISLSH INAYACLVCG KYFQGRGLKS HAYIHSVQFS HHVFLNLHTL KFYCLPDNYE
   181  IIDSSLEDIT YVLKPTFTKQ QIANLDKQAK LSRAYDGTTY LPGIVGLNNI KANDYANAVL
   241  QALSNVPPLR NYFLEEDNYK NIKRPPGDIM FLLVQRFGEL MRKLWNPRNF KAHVSPHEML
   301  QAVVLCSKKT FQITKQGDGV DFLSWFLNAL HSALGGTKKK KKTIVTDVFQ GSMRIFTKKL
   361  PHPDLPAEEK EQLLHNDEYQ ETMVESTFMY LTLDLPTAPL YKDEKEQLII PQVPLFNILA
   421  KFNGITEKEY KTYKENFLKR FQLTKLPPYL IFCIKRFTKN NFFVEKNPTI VNFPITNVDL
   481  REYLSEEVQA VHKNTTYDLI ANIVHDGKPS EGSYRIHVLH HGTGKWYELQ DLQVTDILPQ
   541  MITLSEAYIQ IWKRRDNDET NQQGA

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against USP39 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)
0.35
Highest tissue expression
52 nTPM

Expression across tissuesHPA

Tissue

  • skeletal muscle: 52 nTPM
  • tongue: 40 nTPM
  • bone marrow: 39 nTPM
  • thymus: 38 nTPM
  • tonsil: 30 nTPM
  • blood vessel: 26 nTPM

Single-cell type

  • hepatocytes: 653 nCPM
  • parietal cells: 389 nCPM
  • kupffer cells: 377 nCPM
  • cholangiocytes: 347 nCPM
  • gastric chief cells: 323 nCPM
  • mucous neck cells: 285 nCPM

Immune cell

  • T-reg: 54 nTPM
  • basophil: 51 nTPM
  • MAIT T-cell: 47 nTPM
  • eosinophil: 45 nTPM
  • total PBMC: 44 nTPM
  • intermediate monocyte: 42 nTPM

Brain region

  • choroid plexus: 27 nTPM
  • white matter: 21 nTPM
  • hypothalamus: 21 nTPM
  • medulla oblongata: 20 nTPM
  • thalamus: 19 nTPM
  • cerebellum: 19 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)
0.54
gnomAD pLI
0.01
gnomAD missense Z
1.7
DepMap mean gene effect
-1.57
DepMap dependency class
pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 8% 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

InteractionsUniProt · HPA

Protein binding partners of USP39 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads USP39 as an antibody target. Whether an autoantibody or antibody against USP39 could matter depends on whether native USP39 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

USP39 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 USP39 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

Canonical record: https://seroatlas.com/gene/USP39. 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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