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Aliases for USP28 Gene

Aliases for USP28 Gene

  • Ubiquitin Specific Peptidase 28 2 3 5
  • Ubiquitin-Specific-Processing Protease 28 4
  • Ubiquitin Specific Protease 28 2
  • Deubiquitinating Enzyme 28 4
  • Ubiquitin Thioesterase 28 4
  • EC 3.4.19.12 4
  • EC 3.1.2.15 63
  • KIAA1515 4

External Ids for USP28 Gene

Previous GeneCards Identifiers for USP28 Gene

  • GC11M116021
  • GC11M115180
  • GC11M113702
  • GC11M113206
  • GC11M113173
  • GC11M109597
  • GC11M113668

Summaries for USP28 Gene

Entrez Gene Summary for USP28 Gene

  • The ubiquitin-dependent protein degradation pathway is essential for proteolysis of intracellular proteins and peptides. Enzymes that remove ubiquitin from ubiquitin-conjugated peptides, like USP28, affect the fate and degradation of intracellular proteins and are essential for maintenance of cell-free ubiquitin pools (Valero et al., 2001).[supplied by OMIM, Mar 2008]

GeneCards Summary for USP28 Gene

USP28 (Ubiquitin Specific Peptidase 28) is a Protein Coding gene. Among its related pathways are Ubiquitin-Proteasome Dependent Proteolysis. GO annotations related to this gene include cysteine-type endopeptidase activity and thiol-dependent ubiquitin-specific protease activity. An important paralog of this gene is USP25.

UniProtKB/Swiss-Prot for USP28 Gene

  • Deubiquitinase involved in DNA damage response checkpoint and MYC proto-oncogene stability. Involved in DNA damage induced apoptosis by specifically deubiquitinating proteins of the DNA damage pathway such as CLSPN. Also involved in G2 DNA damage checkpoint, by deubiquitinating CLSPN, and preventing its degradation by the anaphase promoting complex/cyclosome (APC/C). In contrast, it does not deubiquitinate PLK1. Specifically deubiquitinates MYC in the nucleoplasm, leading to prevent MYC degradation by the proteasome: acts by specifically interacting with isoform 1 of FBXW7 (FBW7alpha) in the nucleoplasm and counteracting ubiquitination of MYC by the SCF(FBW7) complex. In contrast, it does not interact with isoform 4 of FBXW7 (FBW7gamma) in the nucleolus, allowing MYC degradation and explaining the selective MYC degradation in the nucleolus. Deubiquitinates ZNF304, hence preventing ZNF304 degradation by the proteasome and leading to the activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) in a subset of colorectal cancers (CRC) cells (PubMed:24623306).

No data available for Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP28 Gene

Genomics for USP28 Gene

Regulatory Elements for USP28 Gene

Enhancers for USP28 Gene
GeneHancer Identifier Score Enhancer Sources TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Other Gene Targets for Enhancer

Enhancers around USP28 on UCSC Golden Path with GeneCards custom track

Promoters for USP28 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USP28 on UCSC Golden Path with GeneCards custom track

Genomic Location for USP28 Gene

Chromosome:
11
Start:
113,797,874 bp from pter
End:
113,875,570 bp from pter
Size:
77,697 bases
Orientation:
Minus strand

Genomic View for USP28 Gene

Genes around USP28 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP28 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP28 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP28 Gene

Proteins for USP28 Gene

  • Protein details for USP28 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q96RU2-UBP28_HUMAN
    Recommended name:
    Ubiquitin carboxyl-terminal hydrolase 28
    Protein Accession:
    Q96RU2
    Secondary Accessions:
    • B0YJC0
    • B0YJC1
    • Q6NZX9
    • Q9P213

    Protein attributes for USP28 Gene

    Size:
    1077 amino acids
    Molecular mass:
    122491 Da
    Quaternary structure:
    • Interacts with ZNF304 (PubMed:24623306). Interacts with PRKD1 (PubMed:24623306). Interacts with TP53BP1 (PubMed:16901786). Interacts with isoform 1 of FBXW7; following DNA damage, dissociates from FBXW7 leading to degradation of MYC (PubMed:17873522, PubMed:17558397) (PubMed:17873522).

    Three dimensional structures from OCA and Proteopedia for USP28 Gene

    Alternative splice isoforms for USP28 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP28 Gene

Proteomics data for USP28 Gene at MOPED

Selected DME Specific Peptides for USP28 Gene

Post-translational modifications for USP28 Gene

  • Degradaded upon nickel ion level or hypoxia exposure.
  • Phosphorylated upon DNA damage at Ser-67 and Ser-714, by ATM or ATR (PubMed:16901786). Phosphorylated by PRKD1 (PubMed:24623306).
  • Ubiquitination at Lys 243
  • Modification sites at PhosphoSitePlus

Antibody Products

  • Cell Signaling Technology (CST) Antibodies for USP28 (USP28)
  • Santa Cruz Biotechnology (SCBT) Antibodies for USP28

Domains & Families for USP28 Gene

Gene Families for USP28 Gene

Suggested Antigen Peptide Sequences for USP28 Gene

Graphical View of Domain Structure for InterPro Entry

Q96RU2

UniProtKB/Swiss-Prot:

UBP28_HUMAN :
  • Contains 1 UIM (ubiquitin-interacting motif) domain.
  • Belongs to the peptidase C19 family. USP28 subfamily.
Domain:
  • Contains 1 UIM (ubiquitin-interacting motif) domain.
  • Contains 1 USP domain.
Family:
  • Belongs to the peptidase C19 family. USP28 subfamily.
genes like me logo Genes that share domains with USP28: view

Function for USP28 Gene

Molecular function for USP28 Gene

UniProtKB/Swiss-Prot CatalyticActivity:
Thiol-dependent hydrolysis of ester, thioester, amide, peptide and isopeptide bonds formed by the C-terminal Gly of ubiquitin (a 76-residue protein attached to proteins as an intracellular targeting signal).
UniProtKB/Swiss-Prot Function:
Deubiquitinase involved in DNA damage response checkpoint and MYC proto-oncogene stability. Involved in DNA damage induced apoptosis by specifically deubiquitinating proteins of the DNA damage pathway such as CLSPN. Also involved in G2 DNA damage checkpoint, by deubiquitinating CLSPN, and preventing its degradation by the anaphase promoting complex/cyclosome (APC/C). In contrast, it does not deubiquitinate PLK1. Specifically deubiquitinates MYC in the nucleoplasm, leading to prevent MYC degradation by the proteasome: acts by specifically interacting with isoform 1 of FBXW7 (FBW7alpha) in the nucleoplasm and counteracting ubiquitination of MYC by the SCF(FBW7) complex. In contrast, it does not interact with isoform 4 of FBXW7 (FBW7gamma) in the nucleolus, allowing MYC degradation and explaining the selective MYC degradation in the nucleolus. Deubiquitinates ZNF304, hence preventing ZNF304 degradation by the proteasome and leading to the activated KRAS-mediated promoter hypermethylation and transcriptional silencing of tumor suppressor genes (TSGs) in a subset of colorectal cancers (CRC) cells (PubMed:24623306).
UniProtKB/Swiss-Prot Induction:
Down-regulated upon hypoxia (PubMed:20046830). Up-regulated by the transcription factor c-Jun/JUN in a KRAS-dependent manner in colorectal cancer (CRC) cells (PubMed:24623306).

Enzyme Numbers (IUBMB) for USP28 Gene

genes like me logo Genes that share phenotypes with USP28: view

Animal Model Products

  • Taconic Biosciences Mouse Models for USP28

Inhibitory RNA Products

In Situ Assay Products

Flow Cytometry Products

No data available for Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for USP28 Gene

Localization for USP28 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP28 Gene

Nucleus, nucleoplasm.

Subcellular locations from

COMPARTMENTS
Jensen Localization Image for USP28 Gene COMPARTMENTS Subcellular localization image for USP28 gene
Compartment Confidence
nucleus 5
cytosol 2

Gene Ontology (GO) - Cellular Components for USP28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005654 nucleoplasm IDA 17558397
GO:0005730 nucleolus IDA --
genes like me logo Genes that share ontologies with USP28: view

Pathways & Interactions for USP28 Gene

genes like me logo Genes that share pathways with USP28: view

Pathways by source for USP28 Gene

1 Qiagen pathway for USP28 Gene

SIGNOR curated interactions for USP28 Gene

Activates:

Gene Ontology (GO) - Biological Process for USP28 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000077 DNA damage checkpoint IMP 18662541
GO:0006511 ubiquitin-dependent protein catabolic process IEA --
GO:0006974 cellular response to DNA damage stimulus IDA 17873522
GO:0008283 cell proliferation IMP 17558397
GO:0010212 response to ionizing radiation IDA 16901786
genes like me logo Genes that share ontologies with USP28: view

Drugs & Compounds for USP28 Gene

(1) Additional Compounds for USP28 Gene - From: HMDB

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
Water
  • Dihydrogen oxide
  • Steam
7732-18-5
genes like me logo Genes that share compounds with USP28: view

Transcripts for USP28 Gene

Unigene Clusters for USP28 Gene

Ubiquitin specific peptidase 28:
Representative Sequences:

Alternative Splicing Database (ASD) splice patterns (SP) for USP28 Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4a · 4b ^ 5 ^ 6 ^ 7 ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12a · 12b ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18a · 18b ^ 19a ·
SP1: - - - - - -
SP2: - - - - - - - -
SP3: - - - - -
SP4: - -
SP5: - - -
SP6: -
SP7:

ExUns: 19b ^ 20 ^ 21 ^ 22 ^ 23 ^ 24 ^ 25 ^ 26 ^ 27 ^ 28a · 28b · 28c
SP1:
SP2: -
SP3:
SP4: -
SP5:
SP6:
SP7:

Relevant External Links for USP28 Gene

GeneLoc Exon Structure for
USP28
ECgene alternative splicing isoforms for
USP28

Expression for USP28 Gene

mRNA expression in normal human tissues for USP28 Gene

mRNA differential expression in normal tissues according to GTEx for USP28 Gene

This gene is overexpressed in Heart - Left Ventricle (x5.6), Muscle - Skeletal (x5.0), and Heart - Atrial Appendage (x4.1).

Protein differential expression in normal tissues from HIPED for USP28 Gene

This gene is overexpressed in Bone (35.2) and Fetal heart (14.7).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MOPED, and MaxQB for USP28 Gene



SOURCE GeneReport for Unigene cluster for USP28 Gene Hs.503891

genes like me logo Genes that share expression patterns with USP28: view

Protein tissue co-expression partners for USP28 Gene

Primer Products

In Situ Assay Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery and mRNA Expression by UniProt/SwissProt for USP28 Gene

Orthologs for USP28 Gene

This gene was present in the common ancestor of animals and fungi.

Orthologs for USP28 Gene

Organism Taxonomy Gene Similarity Type Details
cow
(Bos Taurus)
Mammalia USP28 35
  • 90.71 (n)
  • 93.77 (a)
USP28 36
  • 93 (a)
OneToOne
dog
(Canis familiaris)
Mammalia USP28 35
  • 90.72 (n)
  • 94.13 (a)
USP28 36
  • 95 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp28 35
  • 87.02 (n)
  • 90.72 (a)
Usp28 16
Usp28 36
  • 90 (a)
OneToOne
chimpanzee
(Pan troglodytes)
Mammalia USP28 35
  • 98.67 (n)
  • 98.42 (a)
USP28 36
  • 100 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp28 35
  • 87.79 (n)
  • 91.8 (a)
oppossum
(Monodelphis domestica)
Mammalia USP28 36
  • 47 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP28 36
  • 68 (a)
OneToOne
chicken
(Gallus gallus)
Aves USP28 35
  • 69.09 (n)
  • 68.9 (a)
USP28 36
  • 67 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP28 36
  • 58 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.12044 35
usp28 35
  • 63.75 (n)
  • 64.23 (a)
zebrafish
(Danio rerio)
Actinopterygii usp28 35
  • 61.73 (n)
  • 60.16 (a)
usp28 36
  • 51 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea K02C4.3 36
  • 17 (a)
OneToMany
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes UBP2 38
sea squirt
(Ciona savignyi)
Ascidiacea -- 36
  • 37 (a)
OneToMany
Species with no ortholog for USP28:
  • 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)
  • 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)
  • fruit fly (Drosophila melanogaster)
  • 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)

Evolution for USP28 Gene

ENSEMBL:
Gene Tree for USP28 (if available)
TreeFam:
Gene Tree for USP28 (if available)

Paralogs for USP28 Gene

Paralogs for USP28 Gene

genes like me logo Genes that share paralogs with USP28: view

Variants for USP28 Gene

Sequence variations from dbSNP and Humsavar for USP28 Gene

SNP ID Clin Chr 11 pos Sequence Context AA Info Type
rs1016954 -- 113,810,254(-) ACTGA(A/T)TTGTA intron-variant
rs1016955 -- 113,805,959(-) AGAGT(A/G)AGACC intron-variant
rs1016956 -- 113,805,849(-) ACCCT(A/C)ACCCA intron-variant
rs1034582 -- 113,805,238(-) GTGCC(A/G)GAATG intron-variant
rs1633546 -- 113,803,743(-) CTGTA(C/G)ATGCC intron-variant

Structural Variations from Database of Genomic Variants (DGV) for USP28 Gene

Variant ID Type Subtype PubMed ID
nsv832273 CNV Loss 17160897
nsv497 CNV Insertion 18451855

Variation tolerance for USP28 Gene

Residual Variation Intolerance Score: 3.28% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.89; 35.30% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for USP28 Gene

HapMap Linkage Disequilibrium report
USP28

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP28 Gene

Disorders for USP28 Gene

Relevant External Links for USP28

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP28

No disorders were found for USP28 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP28 Gene

Publications for USP28 Gene

  1. Characterization of alternatively spliced products and tissue- specific isoforms of USP28 and USP25. (PMID: 11597335) Valero R. … Marfany G. (Genome Biol. 2001) 2 3 4 23 67
  2. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente X.S. … Lopez-Otin C. (Nat. Rev. Genet. 2003) 2 3
  3. Proteomic analyses reveal distinct chromatin-associated and soluble transcription factor complexes. (PMID: 25609649) Li X. … Chen J. (Mol. Syst. Biol. 2015) 3
  4. Overexpression of deubiquitinating enzyme USP28 promoted non-small cell lung cancer growth. (PMID: 25656529) Zhang L. … Qian J. (J. Cell. Mol. Med. 2015) 3
  5. The BioPlex Network: A Systematic Exploration of the Human Interactome. (PMID: 26186194) Huttlin E.L. … Gygi S.P. (Cell 2015) 3

Products for USP28 Gene

Sources for USP28 Gene

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