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USP28 ubiquitin specific peptidase 28 [ Homo sapiens (human) ]

Gene ID: 57646, updated on 12-Oct-2019

Summary

Official Symbol
USP28provided by HGNC
Official Full Name
ubiquitin specific peptidase 28provided by HGNC
Primary source
HGNC:HGNC:12625
See related
Ensembl:ENSG00000048028 MIM:610748
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Summary
The protein encoded by this gene is a deubiquitinase involved in the DNA damage pathway and DNA damage-induced apoptosis. Overexpression of this gene is seen in several cancers. [provided by RefSeq, Oct 2016]
Expression
Ubiquitous expression in heart (RPKM 11.8), lymph node (RPKM 4.2) and 24 other tissues See more
Orthologs

Genomic context

See USP28 in Genome Data Viewer
Location:
11q23.2
Exon count:
28
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (113797875..113875572, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (113668597..113746292, complement)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene leucine rich repeat containing 37 member A13, pseudogene Neighboring gene activating transcription factor 4 pseudogene 4 Neighboring gene interferon stimulated exonuclease gene 20 like 2 pseudogene Neighboring gene RNA, U6 small nuclear 1107, pseudogene Neighboring gene Sharpr-MPRA regulatory region 42 Neighboring gene 5-hydroxytryptamine receptor 3B Neighboring gene 5-hydroxytryptamine receptor 3A

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from BioSystems

  • Deubiquitination, organism-specific biosystem (from REACTOME)
    Deubiquitination, organism-specific biosystemUbiquitination, the modification of proteins by the covalent attachment of ubiquitin (Ub), is a key regulatory mechanism for many many cellular processes, including protein degradation by the 26S pro...
  • Metabolism of proteins, organism-specific biosystem (from REACTOME)
    Metabolism of proteins, organism-specific biosystemProtein metabolism comprises the pathways of translation, post-translational modification and protein folding.
  • Post-translational protein modification, organism-specific biosystem (from REACTOME)
    Post-translational protein modification, organism-specific biosystemAfter translation, many newly formed proteins undergo further covalent modifications that alter their functional properties and that are essentially irreversible under physiological conditions in the...
  • Ub-specific processing proteases, organism-specific biosystem (from REACTOME)
    Ub-specific processing proteases, organism-specific biosystemUb-specific processing proteases (USPs) are the largest of the DUB families with more than 50 members in humans. The USP catalytic domain varies considerably in size and consists of six conserved mo...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Homology

Clone Names

  • KIAA1515

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cysteine-type endopeptidase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
 
Process Evidence Code Pubs
DNA damage checkpoint IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA damage checkpoint IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA repair IEA
Inferred from Electronic Annotation
more info
 
Ras protein signal transduction IMP
Inferred from Mutant Phenotype
more info
PubMed 
cell proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to DNA damage stimulus IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to UV IDA
Inferred from Direct Assay
more info
PubMed 
intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
protein deubiquitination IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of protein stability IMP
Inferred from Mutant Phenotype
more info
PubMed 
response to ionizing radiation IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
nuclear body IDA
Inferred from Direct Assay
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 28
Names
deubiquitinating enzyme 28
ubiquitin carboxyl-terminal hydrolase 28 variant 1
ubiquitin thioesterase 28
ubiquitin thiolesterase 28
ubiquitin-specific-processing protease 28
NP_001287958.1
NP_001333181.1
NP_001333182.1
NP_001333183.1
NP_001333184.1
NP_001333186.1
NP_001333187.1
NP_001333188.1
NP_001333189.1
NP_001333190.1
NP_001333191.1
NP_001333192.1
NP_001333193.1
NP_001333194.1
NP_001333196.1
NP_001333197.1
NP_001333198.1
NP_001333199.1
NP_001333200.1
NP_001333201.1
NP_001333202.1
NP_065937.1

NCBI Reference Sequences (RefSeq)

RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051668.1 RefSeqGene

    Range
    4999..82696
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001301029.2NP_001287958.1  ubiquitin carboxyl-terminal hydrolase 28 isoform b

    See identical proteins and their annotated locations for NP_001287958.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), as well as variant 12, encodes isoform b (also known as isoform 2).
    Source sequence(s)
    AK304770, AP001874, AP003170, BC035986, BF434481, DB061316
    Consensus CDS
    CCDS73394.1
    UniProtKB/TrEMBL
    B4E3L3
    Related
    ENSP00000444991.1, ENST00000545540.5
    Conserved Domains (3) summary
    cd02665
    Location:38523
    Peptidase_C19I; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    cl02553
    Location:38142
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam00443
    Location:36273
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. NM_001346252.2NP_001333181.1  ubiquitin carboxyl-terminal hydrolase 28 isoform c

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) encodes the longest isoform (c).
    Source sequence(s)
    AP001874, AP003170, KF459544
  3. NM_001346253.2NP_001333182.1  ubiquitin carboxyl-terminal hydrolase 28 isoform d

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  4. NM_001346254.2NP_001333183.1  ubiquitin carboxyl-terminal hydrolase 28 isoform e

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  5. NM_001346255.2NP_001333184.1  ubiquitin carboxyl-terminal hydrolase 28 isoform f

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  6. NM_001346257.2NP_001333186.1  ubiquitin carboxyl-terminal hydrolase 28 isoform g

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  7. NM_001346258.2NP_001333187.1  ubiquitin carboxyl-terminal hydrolase 28 isoform h

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
    UniProtKB/Swiss-Prot
    Q96RU2
  8. NM_001346259.2NP_001333188.1  ubiquitin carboxyl-terminal hydrolase 28 isoform i

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  9. NM_001346260.2NP_001333189.1  ubiquitin carboxyl-terminal hydrolase 28 isoform j

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  10. NM_001346261.2NP_001333190.1  ubiquitin carboxyl-terminal hydrolase 28 isoform k

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  11. NM_001346262.2NP_001333191.1  ubiquitin carboxyl-terminal hydrolase 28 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (12), as well as variant 2, encodes isoform b.
    Source sequence(s)
    AP001874, AP003170, KF459544
    Consensus CDS
    CCDS73394.1
    UniProtKB/TrEMBL
    B4E3L3
  12. NM_001346263.2NP_001333192.1  ubiquitin carboxyl-terminal hydrolase 28 isoform l

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  13. NM_001346264.2NP_001333193.1  ubiquitin carboxyl-terminal hydrolase 28 isoform m

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  14. NM_001346265.2NP_001333194.1  ubiquitin carboxyl-terminal hydrolase 28 isoform n

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  15. NM_001346267.2NP_001333196.1  ubiquitin carboxyl-terminal hydrolase 28 isoform o

    Status: REVIEWED

    Description
    Transcript Variant: This variant (16), as well as variant 17, encodes isoform o.
    Source sequence(s)
    AP001874, AP003170, KF459544
  16. NM_001346268.2NP_001333197.1  ubiquitin carboxyl-terminal hydrolase 28 isoform o

    Status: REVIEWED

    Description
    Transcript Variant: This variant (17), as well as variant 16, encodes isoform o.
    Source sequence(s)
    AP001874, AP003170, KF459544
    Related
    ENSP00000442431.1, ENST00000544967.5
  17. NM_001346269.2NP_001333198.1  ubiquitin carboxyl-terminal hydrolase 28 isoform p

    Status: REVIEWED

    Description
    Transcript Variant: This variant (18), as well as variants 19 and 20, encodes isoform p.
    Source sequence(s)
    AP001874, AP003170, KF459544
  18. NM_001346270.2NP_001333199.1  ubiquitin carboxyl-terminal hydrolase 28 isoform p

    Status: REVIEWED

    Description
    Transcript Variant: This variant (19), as well as variants 18 and 20, encodes isoform p.
    Source sequence(s)
    AP001874, AP003170, KF459544
  19. NM_001346271.2NP_001333200.1  ubiquitin carboxyl-terminal hydrolase 28 isoform p

    Status: REVIEWED

    Description
    Transcript Variant: This variant (20), as well as variants 18 and 19, encodes isoform p.
    Source sequence(s)
    AP001874, AP003170, KF459544
  20. NM_001346272.2NP_001333201.1  ubiquitin carboxyl-terminal hydrolase 28 isoform q

    Status: REVIEWED

    Source sequence(s)
    AP001874, AP003170, KF459544
  21. NM_001346273.2NP_001333202.1  ubiquitin carboxyl-terminal hydrolase 28 isoform r

    Status: REVIEWED

    Source sequence(s)
    AP001874, BC065928, DB061316
    Consensus CDS
    CCDS86248.1
    UniProtKB/Swiss-Prot
    Q96RU2
    Related
    ENSP00000445743.1, ENST00000537706.5
    Conserved Domains (3) summary
    cd02665
    Location:163397
    Peptidase_C19I; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    cd14355
    Location:2364
    UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins
    cl02553
    Location:163267
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
  22. NM_020886.4NP_065937.1  ubiquitin carboxyl-terminal hydrolase 28 isoform a

    See identical proteins and their annotated locations for NP_065937.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes isoform a (also known as isoform 1).
    Source sequence(s)
    AF266283, AP001874, AP003170, BC035986, BF434481, DB061316
    Consensus CDS
    CCDS31680.1
    UniProtKB/Swiss-Prot
    Q96RU2
    Related
    ENSP00000003302.4, ENST00000003302.8
    Conserved Domains (4) summary
    cd02665
    Location:163648
    Peptidase_C19I; A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl ...
    cd14355
    Location:2364
    UBA_UBP28; UBA domain found in ubiquitin carboxyl-terminal hydrolase 28 (UBP28) and similar proteins
    cl02553
    Location:163267
    Peptidase_C19; Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly ...
    pfam00443
    Location:161398
    UCH; Ubiquitin carboxyl-terminal hydrolase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109.20190905

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    113797875..113875572 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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