Free for academic non-profit institutions. Other users need a Commercial license

Aliases for USP54 Gene

Aliases for USP54 Gene

  • Ubiquitin Specific Peptidase 54 2 3 5
  • Inactive Ubiquitin-Specific Peptidase 54 3 4
  • Ubiquitin Specific Protease 54 2 3
  • C10orf29 3 4
  • Inactive Ubiquitin Carboxyl-Terminal Hydrolase 54 3
  • Chromosome 10 Open Reading Frame 29 2
  • Ubiquitin Specific Proteinase 54 3
  • BA137L10.3 3
  • BA137L10.4 3

External Ids for USP54 Gene

Previous HGNC Symbols for USP54 Gene

  • C10orf29

Previous GeneCards Identifiers for USP54 Gene

  • GC10M074601
  • GC10M074602
  • GC10M074927
  • GC10M075257
  • GC10M069250

Summaries for USP54 Gene

GeneCards Summary for USP54 Gene

USP54 (Ubiquitin Specific Peptidase 54) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include thiol-dependent ubiquitinyl hydrolase activity. An important paralog of this gene is USP53.

UniProtKB/Swiss-Prot for USP54 Gene

  • Has no peptidase activity.

Additional gene information for USP54 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP54 Gene

Genomics for USP54 Gene

GeneHancer (GH) Regulatory Elements for USP54 Gene

Promoters and enhancers for USP54 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH10I073624 Promoter/Enhancer 1.8 Ensembl ENCODE dbSUPER 550.8 +0.1 76 2.6 HDGF PKNOX1 CLOCK SMAD1 ARNT ARID4B NEUROD1 SIN3A DMAP1 ZNF2 ENSG00000268584 USP54 NDST2 SEC24C ZSWIM8 NUDT13 AP3M1 ECD CFAP70 ENSG00000272140
GH10I073575 Promoter/Enhancer 0.8 EPDnew dbSUPER 561 +50.3 50311 0.1 EMSY USP54 GC10P073575 RNU6-883P GC10P073587
GH10I073627 Enhancer 0.4 ENCODE 550.8 -1.5 -1488 0.2 HDGF SCRT2 ENSG00000268584 USP54 ENSG00000272791 GC10P073609
GH10I073588 Enhancer 1.7 FANTOM5 Ensembl ENCODE dbSUPER 16.3 +34.6 34641 5.9 PKNOX1 FOXA2 MLX ZFP64 ARID4B FEZF1 DMAP1 SLC30A9 ZNF766 ZNF213 NUDT13 USP54 RNU6-883P SYNPO2L CAMK2G PPP3CB CFAP70 GC10P073587 GC10P073609
GH10I073584 Enhancer 1.4 Ensembl ENCODE dbSUPER 15.9 +39.6 39612 2.9 PKNOX1 FOXA2 ARID4B FEZF1 DMAP1 ZNF2 YY1 ZNF766 CBX5 ZNF143 GC10P073587 ENSG00000272140 AGAP5 GLUD1P3 SEC24C NUDT13 DUSP8P5 ZSWIM8 BMS1P4 ZSWIM8-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around USP54 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USP54 gene promoter:

Genomic Locations for USP54 Gene

Genomic Locations for USP54 Gene
128,416 bases
Minus strand

Genomic View for USP54 Gene

Genes around USP54 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP54 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP54 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP54 Gene

Proteins for USP54 Gene

  • Protein details for USP54 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Inactive ubiquitin carboxyl-terminal hydrolase 54
    Protein Accession:
    Secondary Accessions:
    • A1L4Q4
    • A3KFK3
    • A3KFK5
    • A3KFK6
    • A3KFK7
    • A6PVS4
    • A6PVS5
    • A6PVS6
    • A6PVS7
    • B3KVY1
    • B9ZVM1
    • Q5F2F4
    • Q6P1N6
    • Q6ZSP1
    • Q6ZSR1
    • Q6ZTM0
    • Q8N1X2

    Protein attributes for USP54 Gene

    1684 amino acids
    Molecular mass:
    187388 Da
    Quaternary structure:
    No Data Available
    • Sequence=BAC04393.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BAG53943.1; Type=Erroneous initiation; Evidence={ECO:0000305}; Sequence=BX649087; Type=Frameshift; Positions=508; Evidence={ECO:0000305}; Sequence=CAO03507.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAO03508.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305}; Sequence=CAO03509.1; Type=Erroneous gene model prediction; Evidence={ECO:0000305};

    Alternative splice isoforms for USP54 Gene

neXtProt entry for USP54 Gene

Post-translational modifications for USP54 Gene

  • Ubiquitination at isoforms=7, 8, 9, 101236

No data available for DME Specific Peptides for USP54 Gene

Domains & Families for USP54 Gene

Gene Families for USP54 Gene

Human Protein Atlas (HPA):
  • Enzymes
  • Predicted intracellular proteins

Protein Domains for USP54 Gene

Suggested Antigen Peptide Sequences for USP54 Gene

GenScript: Design optimal peptide antigens:

Graphical View of Domain Structure for InterPro Entry



  • Belongs to the peptidase C19 family.
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP54: view

Function for USP54 Gene

Molecular function for USP54 Gene

UniProtKB/Swiss-Prot Function:
Has no peptidase activity.

Gene Ontology (GO) - Molecular Function for USP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 16713569
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity IEA --
genes like me logo Genes that share ontologies with USP54: view
genes like me logo Genes that share phenotypes with USP54: view

Animal Models for USP54 Gene

MGI Knock Outs for USP54:

Animal Model Products

miRNA for USP54 Gene

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP54 Gene

Localization for USP54 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP54 gene
Compartment Confidence
mitochondrion 3
nucleus 2
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)

No data available for Subcellular locations from UniProtKB/Swiss-Prot and Gene Ontology (GO) - Cellular Components for USP54 Gene

Pathways & Interactions for USP54 Gene

genes like me logo Genes that share pathways with USP54: view

Pathways by source for USP54 Gene

1 Qiagen pathway for USP54 Gene

Gene Ontology (GO) - Biological Process for USP54 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0016579 protein deubiquitination IEA --
genes like me logo Genes that share ontologies with USP54: view

No data available for SIGNOR curated interactions for USP54 Gene

Drugs & Compounds for USP54 Gene

No Compound Related Data Available

Transcripts for USP54 Gene

Unigene Clusters for USP54 Gene

Ubiquitin specific peptidase 54:
Representative Sequences:

Clone Products

Alternative Splicing Database (ASD) splice patterns (SP) for USP54 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b ^ 8 ^ 9 ^ 10a · 10b ^ 11 ^ 12 ^ 13a · 13b ^ 14a · 14b ^ 15a · 15b ^ 16 ^ 17 ^ 18a ·
SP1: - -
SP2: - - -
SP5: -
SP6: - -

ExUns: 18b · 18c ^ 19a · 19b ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b ^ 23 ^ 24a · 24b · 24c
SP2: - - - -
SP4: -
SP6: - -
SP7: - - -
SP10: -

Relevant External Links for USP54 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for USP54 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP54 Gene

mRNA differential expression in normal tissues according to GTEx for USP54 Gene

This gene is overexpressed in Muscle - Skeletal (x7.3).

Protein differential expression in normal tissues from HIPED for USP54 Gene

This gene is overexpressed in Prostate (30.7), Frontal cortex (28.7), and Spinal cord (6.4).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for USP54 Gene

Protein tissue co-expression partners for USP54 Gene

NURSA nuclear receptor signaling pathways regulating expression of USP54 Gene:


SOURCE GeneReport for Unigene cluster for USP54 Gene:


mRNA Expression by UniProt/SwissProt for USP54 Gene:

Tissue specificity: Weakly expressed in a few tissues.

Evidence on tissue expression from TISSUES for USP54 Gene

  • Nervous system(4.6)
  • Lung(4.3)
  • Skin(4.2)
genes like me logo Genes that share expression patterns with USP54: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP54 Gene

Orthologs for USP54 Gene

This gene was present in the common ancestor of animals.

Orthologs for USP54 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia USP54 33 34
  • 98.79 (n)
(Canis familiaris)
Mammalia USP54 33 34
  • 90.48 (n)
(Bos Taurus)
Mammalia USP54 33 34
  • 89.62 (n)
(Mus musculus)
Mammalia Usp54 33 16 34
  • 83.75 (n)
(Rattus norvegicus)
Mammalia Usp54 33
  • 83.09 (n)
(Monodelphis domestica)
Mammalia USP54 34
  • 70 (a)
(Ornithorhynchus anatinus)
Mammalia USP54 34
  • 62 (a)
(Gallus gallus)
Aves USP54 33 34
  • 67.65 (n)
(Anolis carolinensis)
Reptilia USP54 34
  • 57 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia usp54 33
  • 61.45 (n)
(Danio rerio)
Actinopterygii usp54a 33 34
  • 65.98 (n)
USP54 (1 of 2) 34
  • 49 (a)
fruit fly
(Drosophila melanogaster)
Insecta ec 34
  • 15 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 55 (a)
Species where no ortholog for USP54 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for USP54 Gene

Gene Tree for USP54 (if available)
Gene Tree for USP54 (if available)

Paralogs for USP54 Gene

Paralogs for USP54 Gene

(1) SIMAP similar genes for USP54 Gene using alignment to 6 proteins:

genes like me logo Genes that share paralogs with USP54: view

Variants for USP54 Gene

Sequence variations from dbSNP and Humsavar for USP54 Gene

SNP ID Clin Chr 10 pos Variation AA Info Type
VAR_036360 A breast cancer sample p.Leu505Val
rs1000031081 -- 73,604,270(-) C/T genic_upstream_transcript_variant, intron_variant
rs1000034890 -- 73,574,555(-) T/C genic_upstream_transcript_variant, intron_variant
rs1000097938 -- 73,602,990(-) G/A genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000106526 -- 73,574,334(-) A/G genic_upstream_transcript_variant, intron_variant

Structural Variations from Database of Genomic Variants (DGV) for USP54 Gene

Variant ID Type Subtype PubMed ID
esv3623815 CNV loss 21293372
esv3623814 CNV loss 21293372
esv2430194 CNV deletion 19546169

Variation tolerance for USP54 Gene

Residual Variation Intolerance Score: 42.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 4.80; 66.87% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP54 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP54 Gene

Disorders for USP54 Gene

Additional Disease Information for USP54

Genetic Association Database
Human Genome Epidemiology Navigator
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for USP54 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP54 Gene

Publications for USP54 Gene

  1. Cloning and enzymatic analysis of 22 novel human ubiquitin-specific proteases. (PMID: 14715245) Quesada V … López-Otín C (Biochemical and biophysical research communications 2004) 2 3 4 58
  2. A scan of chromosome 10 identifies a novel locus showing strong association with late-onset Alzheimer disease. (PMID: 16385451) Grupe A … Goate A (American journal of human genetics 2006) 3 44 58
  3. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  4. The DNA sequence and comparative analysis of human chromosome 10. (PMID: 15164054) Deloukas P … Rogers J (Nature 2004) 3 4 58
  5. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58

Products for USP54 Gene

Sources for USP54 Gene

Loading form....