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

    Gene ID: 9960, updated on 6-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
    NEW
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    Try the new Transcript table

    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)

    NEW Try the new Transcript table

    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