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

Gene ID: 10713, updated on 10-Oct-2019

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
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
Expression
Ubiquitous expression in bone marrow (RPKM 14.6), placenta (RPKM 13.8) and 25 other tissues See more
Orthologs

Genomic context

See USP39 in Genome Data Viewer
Location:
2p11.2
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190905 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (85602843..85649284)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (85829965..85876407)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ring finger protein 181 Neighboring gene transmembrane protein 150A Neighboring gene chromosome 2 open reading frame 68 Neighboring gene surfactant protein B 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 BioSystems

  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • Spliceosome, organism-specific biosystem (from KEGG)
    Spliceosome, organism-specific biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, conserved biosystem (from KEGG)
    Spliceosome, conserved biosystemAfter transcription, eukaryotic mRNA precursors contain protein-coding exons and noncoding introns. In the following splicing, introns are excised and exons are joined by a macromolecular complex, th...
  • Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, organism-specific biosystemStructural complex; Genetic information processing; Spliceosome
  • Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystem (from KEGG)
    Spliceosome, U4/U6.U5 tri-snRNP, conserved biosystemStructural complex; Genetic information processing; Spliceosome
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ33136, MGC75069

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
thiol-dependent ubiquitinyl hydrolase activity IEA
Inferred from Electronic Annotation
more info
 
zinc ion binding IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
RNA splicing TAS
Traceable Author Statement
more info
PubMed 
cell cycle IEA
Inferred from Electronic Annotation
more info
 
cell division IEA
Inferred from Electronic Annotation
more info
 
mRNA processing TAS
Traceable Author Statement
more info
PubMed 
mRNA splicing, via spliceosome IDA
Inferred from Direct Assay
more info
PubMed 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
protein deubiquitination IEA
Inferred from Electronic Annotation
more info
 
spliceosomal complex assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
U4/U6 x U5 tri-snRNP complex IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
spliceosomal complex IEA
Inferred from Electronic Annotation
more info
 

General protein information

Preferred Names
U4/U6.U5 tri-snRNP-associated protein 2
Names
SAD1 homolog
SnRNP assembly defective 1 homolog
U4/U6.U5 tri-snRNP-associated 65 kDa protein
inactive ubiquitin-specific peptidase 39
small nuclear ribonucleoprotein 65kDa (U4/U6.U5)
ubiquitin specific protease 39

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_001256725.2NP_001243654.1  U4/U6.U5 tri-snRNP-associated protein 2 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
    Q53GS9
    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  U4/U6.U5 tri-snRNP-associated protein 2 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/Swiss-Prot
    Q53GS9
    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_001256727.1NP_001243656.1  U4/U6.U5 tri-snRNP-associated protein 2 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)
    AI201523, AK001772, AK302236, BC001384, DB444135
    Consensus CDS
    CCDS74534.1
    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    A0A087X1B2, B3KMG1, 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_001256728.1NP_001243657.1  U4/U6.U5 tri-snRNP-associated protein 2 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, AI201523, AK295257, BC001384, DB444135
    Consensus CDS
    CCDS58716.1
    UniProtKB/Swiss-Prot
    Q53GS9
    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  U4/U6.U5 tri-snRNP-associated protein 2 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
    Q53GS9
    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: Homo sapiens Annotation Release 109.20190905

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    85602843..85649284
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_006711922.2XP_006711985.1  U4/U6.U5 tri-snRNP-associated protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006711985.1

    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    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_011532488.1XP_011530790.1  U4/U6.U5 tri-snRNP-associated protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011530790.1

    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    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 ...
  3. XM_006711923.2XP_006711986.1  U4/U6.U5 tri-snRNP-associated protein 2 isoform X1

    See identical proteins and their annotated locations for XP_006711986.1

    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    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 ...
  4. XM_011532487.1XP_011530789.1  U4/U6.U5 tri-snRNP-associated protein 2 isoform X1

    See identical proteins and their annotated locations for XP_011530789.1

    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    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 ...
  5. XM_017003182.1XP_016858671.1  U4/U6.U5 tri-snRNP-associated protein 2 isoform X1

    UniProtKB/Swiss-Prot
    Q53GS9
    UniProtKB/TrEMBL
    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 ...

RNA

  1. XR_001738593.1 RNA Sequence

  2. XR_939652.2 RNA Sequence

  3. XR_939653.2 RNA Sequence

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