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

Gene ID: 9960, updated on 17-Jun-2024

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; AllianceGenome:HGNC:12626
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
Summary
Enables histone binding activity and thiol-dependent deubiquitinase. Involved in several processes, including DNA repair; histone deubiquitination; and regulation of protein stability. Located in several cellular components, including Flemming body; cytoplasmic ribonucleoprotein granule; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Ubiquitous expression in bone marrow (RPKM 9.8), spleen (RPKM 5.3) and 25 other tissues See more
Orthologs
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Genomic context

See USP3 in Genome Data Viewer
Location:
15q22.31
Exon count:
20
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (63504593..63594633)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (61311846..61401872)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (63796792..63886832)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124903506 Neighboring gene uncharacterized LOC124903505 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63630428-63631324 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:63637609-63637796 Neighboring gene Neanderthal introgressed variant-containing enhancer experimental_40513 Neighboring gene carbonic anhydrase 12 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63673729-63674249 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63674250-63674769 Neighboring gene long intergenic non-protein coding RNA 2568 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9529 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9530 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9531 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9532 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9533 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9535 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6515 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9536 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9537 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:63795072-63795865 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr15:63795866-63796658 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6519 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6517 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6518 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9539 Neighboring gene Sharpr-MPRA regulatory region 15501 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:63851884-63852437 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr15:63882664-63883863 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9540 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63892143-63892860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:63893123-63893940 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 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:63958187-63958357 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64006451-64006952 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64006953-64007452 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:64014173-64014349 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64057331-64058088 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:64058904-64059404 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6522 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:64107893-64108654 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:64114122-64114622 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:64125303-64126168

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

EBI 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.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • MGC129878, MGC129879

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding IEA
Inferred from Electronic Annotation
more info
 
enables cysteine-type deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H2A deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone H2B deubiquitinase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
enables histone binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables promoter-specific chromatin binding IEA
Inferred from Electronic Annotation
more info
 
enables zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in DNA repair-dependent chromatin remodeling IDA
Inferred from Direct Assay
more info
PubMed 
involved_in negative regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
involved_in proteolysis IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Flemming body IDA
Inferred from Direct Assay
more info
 
part_of chromatin IDA
Inferred from Direct Assay
more info
PubMed 
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
 
located_in nucleoplasm TAS
Traceable Author Statement
more info
 
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
 

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_047289349.1
XP_047289350.1
XP_047289351.1
XP_054235272.1
XP_054235273.1
XP_054235274.1
XP_054235275.1
XP_054235276.1
XP_054235277.1

NCBI Reference Sequences (RefSeq)

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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_001256702.2NP_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/TrEMBL
    H0YKU8
    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
    B4DVU5, F5H1A6, Q8WVD0, Q9Y6I4
    UniProtKB/TrEMBL
    H0YMI4
    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: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000015.10 Reference GRCh38.p14 Primary Assembly

    Range
    63504593..63594633
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047433394.1XP_047289350.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
    Related
    ENSP00000268049.7, ENST00000268049.11
  2. XM_047433393.1XP_047289349.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  3. XM_017022765.2XP_016878254.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, 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_017022763.2XP_016878252.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, 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
  5. XM_017022764.2XP_016878253.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, 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_047433395.1XP_047289351.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

    UniProtKB/TrEMBL
    H0YKU8
    Related
    ENSP00000452947.1, ENST00000559257.5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060939.1 Alternate T2T-CHM13v2.0

    Range
    61311846..61401872
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054379299.1XP_054235274.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  2. XM_054379300.1XP_054235275.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  3. XM_054379298.1XP_054235273.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  4. XM_054379297.1XP_054235272.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  5. XM_054379301.1XP_054235276.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X1

    UniProtKB/TrEMBL
    E9PE27, H0YMI4, Q6JHV3
  6. XM_054379302.1XP_054235277.1  ubiquitin carboxyl-terminal hydrolase 3 isoform X2

    UniProtKB/TrEMBL
    H0YKU8