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USP3 ubiquitin specific peptidase 3 [ Homo sapiens (human) ]

Gene ID: 9960, updated on 3-May-2020

Summary

Official Symbol
USP3provided by HGNC
Official Full Name
ubiquitin specific peptidase 3provided by HGNC
Primary source
HGNC:HGNC:12626
See related
Ensembl:ENSG00000140455 MIM:604728
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
UBP; SIH003
Expression
Ubiquitous expression in bone marrow (RPKM 9.8), spleen (RPKM 5.3) and 25 other tissues See more
Orthologs

Genomic context

See USP3 in Genome Data Viewer
Location:
15q22.31
Exon count:
21
Annotation release Status Assembly Chr Location
109.20200228 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (63504511..63594640)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (63796710..63886839)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene carbonic anhydrase 12 Neighboring gene long intergenic non-protein coding RNA 2568 Neighboring gene USP3 antisense RNA 1 Neighboring gene F-box and leucine rich repeat protein 22 Neighboring gene HECT and RLD domain containing E3 ubiquitin protein ligase family member 1

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?

Phenotypes

NHGRI GWAS Catalog

Description
Association of genome-wide variation with the risk of incident heart failure in adults of European and African ancestry: a prospective meta-analysis from the cohorts for heart and aging research in genomic epidemiology (CHARGE) consortium.
NHGRI GWA Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • MGC129878, MGC129879

Gene Ontology Provided by GOA

Function Evidence Code Pubs
RNA polymerase II proximal promoter sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
more info
 
thiol-dependent ubiquitin-specific protease activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
histone deubiquitination IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone deubiquitination IDA
Inferred from Direct Assay
more info
PubMed 
mitotic cell cycle IMP
Inferred from Mutant Phenotype
more info
PubMed 
negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
protein deubiquitination TAS
Traceable Author Statement
more info
 
regulation of protein stability IDA
Inferred from Direct Assay
more info
PubMed 
ubiquitin-dependent protein catabolic process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Flemming body IDA
Inferred from Direct Assay
more info
 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
 
nuclear chromatin IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
ubiquitin carboxyl-terminal hydrolase 3
Names
deubiquitinating enzyme 3
ubiquitin thioesterase 3
ubiquitin thiolesterase 3
ubiquitin-specific-processing protease 3
NP_001243631.1
NP_006528.2
XP_016878252.1
XP_016878253.1
XP_016878254.1
XP_016878255.1
XP_016878256.1
XP_016878257.1

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_001256702.1NP_001243631.1  ubiquitin carboxyl-terminal hydrolase 3 isoform 2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 5' coding region, but maintains the reading frame, compared to variant 1. The encoded isoform (2) is shorter than isoform 1.
    Source sequence(s)
    AC118274, AK301236, BC065300, DA557812
    Consensus CDS
    CCDS58370.1
    UniProtKB/Swiss-Prot
    Q9Y6I4
    Related
    ENSP00000445828.1, ENST00000540797.5
    Conserved Domains (3) summary
    cl02553
    Location:116465
    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:114464
    UCH; Ubiquitin carboxyl-terminal hydrolase
    cl09957
    Location:2953
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  2. NM_006537.4NP_006528.2  ubiquitin carboxyl-terminal hydrolase 3 isoform 1

    See identical proteins and their annotated locations for NP_006528.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC118274, AK314223
    Consensus CDS
    CCDS32265.1
    UniProtKB/Swiss-Prot
    Q9Y6I4
    Related
    ENSP00000369681.3, ENST00000380324.8
    Conserved Domains (2) summary
    pfam00443
    Location:159508
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam02148
    Location:29105
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein

RNA

  1. NR_046341.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC118274, AY461579, DA557812
  2. NR_046342.2 RNA Sequence

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) includes an alternate internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
    Source sequence(s)
    AC118274, BC065300, BX647760, DA557812
    Related
    ENST00000559192.5

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    63504511..63594640
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_017022766.1XP_016878255.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

    Related
    ENSP00000452947.1, ENST00000559257.5
  2. XM_017022767.1XP_016878256.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

  3. XM_017022763.1XP_016878252.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    Q6JHV3
    Conserved Domains (3) summary
    cl02553
    Location:138487
    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:136486
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam02148
    Location:883
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  4. XM_017022768.1XP_016878257.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X3

    Conserved Domains (2) summary
    cl02553
    Location:1340
    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:1339
    UCH; Ubiquitin carboxyl-terminal hydrolase
  5. XM_017022764.1XP_016878253.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    Q6JHV3
    Conserved Domains (3) summary
    cl02553
    Location:138487
    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:136486
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam02148
    Location:883
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
  6. XM_017022765.1XP_016878254.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    Q6JHV3
    Related
    ENSP00000268049.7, ENST00000268049.11
    Conserved Domains (3) summary
    cl02553
    Location:138487
    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:136486
    UCH; Ubiquitin carboxyl-terminal hydrolase
    pfam02148
    Location:883
    zf-UBP; Zn-finger in ubiquitin-hydrolases and other protein
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