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USP21 ubiquitin specific peptidase 21 [ Homo sapiens (human) ]

Gene ID: 27005, updated on 6-Oct-2019

Summary

Official Symbol
USP21provided by HGNC
Official Full Name
ubiquitin specific peptidase 21provided by HGNC
Primary source
HGNC:HGNC:12620
See related
Ensembl:ENSG00000143258 MIM:604729
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
Also known as
USP16; USP23
Summary
This gene encodes a member of the C19 peptidase family, also known as family 2 of ubiquitin carboxy-terminal hydrolases. The encoded protein cleaves ubiquitin from ubiquitinated proteins for recycling in intracellular protein degradation. The encoded protein is also able to release NEDD8, a ubiquitin-like protein, from NEDD8-conjugated proteins. This gene has been referred to as USP16 and USP23 but is now known as USP21. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Feb 2016]
Expression
Ubiquitous expression in ovary (RPKM 11.4), testis (RPKM 9.2) and 25 other tissues See more
Orthologs

Genomic context

See USP21 in Genome Data Viewer
Location:
1q23.3
Exon count:
13
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (161159487..161165752)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (161129248..161135516)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene nitrilase 1 Neighboring gene death effector domain containing Neighboring gene linc-UFC1 Neighboring gene ubiquitin-fold modifier conjugating enzyme 1 Neighboring gene protoporphyrinogen oxidase Neighboring gene beta-1,4-galactosyltransferase 3 Neighboring gene ADAM metallopeptidase with thrombospondin type 1 motif 4 Neighboring gene NADH:ubiquinone oxidoreductase core subunit S2

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

  • Death Receptor Signalling, organism-specific biosystem (from REACTOME)
    Death Receptor Signalling, organism-specific biosystemThe death receptors, all cell-surface receptors, begin the process of caspase activation. The common feature of these type 1 transmembrane proteins is the "death-domain" a conserved cytoplasmic motif...
  • 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...
  • Integrated Breast Cancer Pathway, organism-specific biosystem (from WikiPathways)
    Integrated Breast Cancer Pathway, organism-specific biosystemThis pathway incorporates the most important proteins for Breast Cancer. The Rp score from the Connectivity-Maps (C-Maps) webserver was used to determine the rank of the most important proteins in Br...
  • 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...
  • Regulation of TNFR1 signaling, organism-specific biosystem (from REACTOME)
    Regulation of TNFR1 signaling, organism-specific biosystemTumor necrosis factor-alpha (TNFalpha) is an inflammatory cytokine, that activates either cell survival (e.g.,inflammation, proliferation) or cell death upon association with TNF receptor 1 (TNFR1). ...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • TNF signaling, organism-specific biosystem (from REACTOME)
    TNF signaling, organism-specific biosystemThe inflammatory cytokine tumor necrosis factor alpha (TNF-alpha) is expressed in immune and nonimmune cell types including macrophages, T cells, mast cells, granulocytes, natural killer (NK) cells, ...
  • TNFR1-induced NFkappaB signaling pathway, organism-specific biosystem (from REACTOME)
    TNFR1-induced NFkappaB signaling pathway, organism-specific biosystemActivation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce inflammation, cell proliferation, survival or cell death (Ward C et al. 1999; Michea...
  • TNFR1-induced proapoptotic signaling, organism-specific biosystem (from REACTOME)
    TNFR1-induced proapoptotic signaling, organism-specific biosystemActivation of tumor necrosis factor receptor 1 (TNFR1) can trigger multiple signal transduction pathways to induce cell survival or cell death (Ward C et al. 1999; Micheau O and Tschopp J 2003; Wider...
  • 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

Markers

Homology

Clone Names

  • MGC3394

Gene Ontology Provided by GOA

Function Evidence Code Pubs
NEDD8-specific protease activity IDA
Inferred from Direct Assay
more info
PubMed 
cysteine-type peptidase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
cysteine-type peptidase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IDA
Inferred from Direct Assay
more info
PubMed 
thiol-dependent ubiquitin-specific protease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity IDA
Inferred from Direct Assay
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
thiol-dependent ubiquitinyl hydrolase activity TAS
Traceable Author Statement
more info
PubMed 
transcription coactivator activity ISS
Inferred from Sequence or Structural Similarity
more info
 
Process Evidence Code Pubs
histone deubiquitination ISS
Inferred from Sequence or Structural Similarity
more info
 
neuron projection development IEA
Inferred from Electronic Annotation
more info
 
positive regulation of transcription, DNA-templated ISS
Inferred from Sequence or Structural Similarity
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytosol IDA
Inferred from Direct Assay
more info
 
cytosol TAS
Traceable Author Statement
more info
 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
plasma membrane IDA
Inferred from Direct Assay
more info
 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 21
Names
NEDD8-specific protease
deubiquitinating enzyme 21
ubiquitin specific protease 21
ubiquitin thioesterase 21
ubiquitin thiolesterase 21
ubiquitin-specific processing protease 21
ubiquitin-specific protease 16
NP_001014443.1
NP_001306776.1
NP_001306777.1
NP_036607.3
XP_016856525.1
XP_016856526.1
XP_016856527.1
XP_016856528.1
XP_016856529.1
XP_016856530.1
XP_024302181.1

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.

mRNA and Protein(s)

  1. NM_001014443.3NP_001014443.1  ubiquitin carboxyl-terminal hydrolase 21 isoform c

    See identical proteins and their annotated locations for NP_001014443.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence compared to variant 4. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 1 and 3 both encode the same isoform (c).
    Source sequence(s)
    AF177758, AI038040, BC090946, BI755746
    Consensus CDS
    CCDS30920.1
    UniProtKB/Swiss-Prot
    Q9UK80
    Related
    ENSP00000356981.3, ENST00000368002.8
    Conserved Domains (2) summary
    cd02674
    Location:213556
    Peptidase_C19R; 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 ...
    pfam00443
    Location:212555
    UCH; Ubiquitin carboxyl-terminal hydrolase
  2. NM_001319847.2NP_001306776.1  ubiquitin carboxyl-terminal hydrolase 21 isoform a

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) encodes the longest isoform (a).
    Source sequence(s)
    AI038040, AK310326, DA000829
    Conserved Domains (2) summary
    cd02674
    Location:242585
    Peptidase_C19R; 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 ...
    pfam00443
    Location:241584
    UCH; Ubiquitin carboxyl-terminal hydrolase
  3. NM_001319848.2NP_001306777.1  ubiquitin carboxyl-terminal hydrolase 21 isoform b

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence and uses an alternate in-frame splice junction in the 3' end compared to variant 4. The resulting isoform (b) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.
    Source sequence(s)
    AF217979, AF233442, AI038040, DA000829
    Consensus CDS
    CCDS81392.1
    UniProtKB/Swiss-Prot
    Q9UK80
    Related
    ENSP00000356980.1, ENST00000368001.1
    Conserved Domains (3) summary
    cd02674
    Location:213542
    Peptidase_C19R; 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:212346
    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:212541
    UCH; Ubiquitin carboxyl-terminal hydrolase
  4. NM_012475.5NP_036607.3  ubiquitin carboxyl-terminal hydrolase 21 isoform c

    See identical proteins and their annotated locations for NP_036607.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence compared to variant 4. The resulting isoform (c) is shorter at the N-terminus compared to isoform a. Variants 1 and 3 both encode the same isoform (c).
    Source sequence(s)
    AF177758, AI038040, BI755746
    Consensus CDS
    CCDS30920.1
    UniProtKB/Swiss-Prot
    Q9UK80
    Related
    ENSP00000289865.8, ENST00000289865.12
    Conserved Domains (2) summary
    cd02674
    Location:213556
    Peptidase_C19R; 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 ...
    pfam00443
    Location:212555
    UCH; Ubiquitin carboxyl-terminal hydrolase

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    161159487..161165752
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017001037.2XP_016856526.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X2

  2. XM_017001039.2XP_016856528.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X2

  3. XM_017001036.1XP_016856525.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X1

  4. XM_017001040.1XP_016856529.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X3

    Conserved Domains (2) summary
    cd02674
    Location:242585
    Peptidase_C19R; 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 ...
    pfam00443
    Location:241584
    UCH; Ubiquitin carboxyl-terminal hydrolase
  5. XM_017001038.2XP_016856527.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X2

  6. XM_024446413.1XP_024302181.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X5

    Conserved Domains (1) summary
    cd02674
    Location:53321
    Peptidase_C19R; 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 ...
  7. XM_017001041.1XP_016856530.1  ubiquitin carboxyl-terminal hydrolase 21 isoform X4

RNA

  1. XR_002956280.1 RNA Sequence

  2. XR_002956279.1 RNA Sequence

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