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    USP39 ubiquitin specific peptidase 39 [ Homo sapiens (human) ]

    Gene ID: 10713, updated on 5-May-2024

    Summary

    Official Symbol
    USP39provided by HGNC
    Official Full Name
    ubiquitin specific peptidase 39provided by HGNC
    Primary source
    HGNC:HGNC:20071
    See related
    Ensembl:ENSG00000168883 MIM:611594; AllianceGenome:HGNC:20071
    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
    65K; SAD1; CGI-21; HSPC332; SNRNP65
    Summary
    Predicted to enable thiol-dependent deubiquitinase and zinc ion binding activity. Involved in spliceosomal complex assembly. Located in nucleoplasm. Part of U4/U6 x U5 tri-snRNP complex. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in bone marrow (RPKM 14.6), placenta (RPKM 13.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See USP39 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (85602861..85649283)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (85604921..85651339)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85829984..85876406)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11704 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11705 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 11706 Neighboring gene ring finger protein 181 Neighboring gene transmembrane protein 150A Neighboring gene chromosome 2 open reading frame 68 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:85838960-85839341 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16134 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:85839517-85839689 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16135 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16136 Neighboring gene surfactant protein B Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16137 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 16138 Neighboring gene uncharacterized LOC105374842

    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?

    HIV-1 interactions

    Replication interactions

    Interaction Pubs
    Knockdown of ubiquitin specific peptidase 39 (USP39) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev HIV-1 Rev interacting protein, ubiquitin specific peptidase 39 (USP39), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with USP39 is increased by RRE PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Clone Names

    • FLJ33136, MGC75069

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    NOT enables cysteine-type deubiquitinase activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in RNA splicing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in cell division IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mRNA processing TAS
    Traceable Author Statement
    more info
    PubMed 
    involved_in mRNA splicing, via spliceosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in mRNA splicing, via spliceosome NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in spliceosomal complex assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of U4/U6 x U5 tri-snRNP complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of U4/U6 x U5 tri-snRNP complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in nucleus NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of spliceosomal complex IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    ubiquitin carboxyl-terminal hydrolase 39
    Names
    SAD1 homolog
    SnRNP assembly defective 1 homolog
    U4/U6.U5 tri-snRNP-associated 65 kDa protein
    U4/U6.U5 tri-snRNP-associated protein 2
    inactive ubiquitin-specific peptidase 39
    small nuclear ribonucleoprotein 65kDa (U4/U6.U5)
    ubiquitin specific protease 39
    NP_001243654.1
    NP_001243655.1
    NP_001243656.1
    NP_001243657.1
    NP_006581.2
    XP_006711985.1
    XP_047298943.1
    XP_047298944.1
    XP_054196188.1
    XP_054196189.1
    XP_054196190.1
    XP_054196191.1

    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_001256725.2NP_001243654.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 1

      See identical proteins and their annotated locations for NP_001243654.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) uses an alternate splice site in the 3' UTR, compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AI201523, BC067273
      Consensus CDS
      CCDS33234.1
      UniProtKB/Swiss-Prot
      A8K086, B3KM40, B4DHT4, D6W5L4, G5E9H0, Q53GS9, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310
      UniProtKB/TrEMBL
      B9A018
      Related
      ENSP00000386864.1, ENST00000409470.5
      Conserved Domains (1) summary
      cd02669
      Location:106553
      Peptidase_C19M; 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 ...
    2. NM_001256726.2NP_001243655.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 2

      See identical proteins and their annotated locations for NP_001243655.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks an exon in the 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is shorter and has a distinct C-terminus, compared to isoform 1.
      Source sequence(s)
      AI201523, AK001047, AL519827, DB124294
      Consensus CDS
      CCDS58717.1
      UniProtKB/TrEMBL
      B9A018
      Related
      ENSP00000386803.3, ENST00000409766.7
      Conserved Domains (2) summary
      cd02669
      Location:106477
      Peptidase_C19M; 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:224476
      UCH; Ubiquitin carboxyl-terminal hydrolase
    3. NM_001256727.2NP_001243656.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK001772, AK302236, BC001384, DB444135
      Consensus CDS
      CCDS74534.1
      UniProtKB/TrEMBL
      A0A087X1B2, B7Z7L9
      Related
      ENSP00000484024.1, ENST00000613444.4
      Conserved Domains (1) summary
      cd02669
      Location:28475
      Peptidase_C19M; 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 ...
    4. NM_001256728.2NP_001243657.1  ubiquitin carboxyl-terminal hydrolase 39 isoform 4

      See identical proteins and their annotated locations for NP_001243657.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR, lacks a portion of the 5' coding region, initiates translation at an alternate start codon, and lacks an in-frame exon in the 5' coding region, compared to variant 1. The encoded isoform (4) is shorter and has a distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AF161450, AK295257, BC001384
      Consensus CDS
      CCDS58716.1
      UniProtKB/TrEMBL
      B7Z7L9
      Related
      ENSP00000396133.2, ENST00000450066.6
      Conserved Domains (1) summary
      cd02669
      Location:28450
      Peptidase_C19M; 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 ...
    5. NM_006590.4NP_006581.2  ubiquitin carboxyl-terminal hydrolase 39 isoform 1

      See identical proteins and their annotated locations for NP_006581.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AK289451, BC001384
      Consensus CDS
      CCDS33234.1
      UniProtKB/Swiss-Prot
      A8K086, B3KM40, B4DHT4, D6W5L4, G5E9H0, Q53GS9, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310
      UniProtKB/TrEMBL
      B9A018
      Related
      ENSP00000312981.6, ENST00000323701.11
      Conserved Domains (1) summary
      cd02669
      Location:106553
      Peptidase_C19M; 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 ...

    RNA

    1. NR_046347.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (6) uses an alternate 5'-most exon compared to variant 1. This variant is represented as non-coding due to the presence of an upstream ORF that is predicted to interfere with translation of the longest ORF; translation of the upstream ORF renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI201523, AK056334, DA548921
      Related
      ENST00000459775.5

    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_000002.12 Reference GRCh38.p14 Primary Assembly

      Range
      85602861..85649283
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_006711922.3XP_006711985.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X3

      See identical proteins and their annotated locations for XP_006711985.1

      UniProtKB/TrEMBL
      B3KMG1, B3KPG7
      Conserved Domains (1) summary
      cl02553
      Location:1284
      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 ...
    2. XM_047442988.1XP_047298944.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X2

      UniProtKB/TrEMBL
      A0A087X1B2
    3. XM_047442987.1XP_047298943.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060926.1 Alternate T2T-CHM13v2.0

      Range
      85604921..85651339
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054340215.1XP_054196190.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X3

      UniProtKB/TrEMBL
      B3KPG7
    2. XM_054340214.1XP_054196189.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X2

      UniProtKB/TrEMBL
      A0A087X1B2
    3. XM_054340213.1XP_054196188.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X1

    4. XM_054340216.1XP_054196191.1  ubiquitin carboxyl-terminal hydrolase 39 isoform X3

      UniProtKB/TrEMBL
      B3KPG7