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Aliases for USP39 Gene

Aliases for USP39 Gene

  • Ubiquitin Specific Peptidase 39 2 3 5
  • Small Nuclear Ribonucleoprotein 65kDa (U4/U6.U5) 2 3
  • U4/U6.U5 Tri-SnRNP-Associated 65 KDa Protein 3 4
  • Inactive Ubiquitin-Specific Peptidase 39 3 4
  • Ubiquitin Specific Protease 39 2 3
  • SAD1 Homolog 3 4
  • 65K 3 4
  • SnRNP Assembly Defective 1 Homolog (S.Cerevisiae) 2
  • U4/U6.U5 Tri-SnRNP-Associated Protein 2 3
  • SnRNP Assembly Defective 1 Homolog 3
  • HSPC332 3
  • SNRNP65 3
  • CGI-21 3
  • SAD1 3

External Ids for USP39 Gene

Previous GeneCards Identifiers for USP39 Gene

  • GC02P085787
  • GC02P085804
  • GC02P085817
  • GC02P085754
  • GC02P085829
  • GC02P085604
  • GC02P085608
  • GC02P085610
  • GC02P085612
  • GC02P085614
  • GC02P085616
  • GC02P085618
  • GC02P085622

Summaries for USP39 Gene

GeneCards Summary for USP39 Gene

USP39 (Ubiquitin Specific Peptidase 39) is a Protein Coding gene. Among its related pathways are mRNA Splicing - Major Pathway and Ubiquitin-Proteasome Dependent Proteolysis. Gene Ontology (GO) annotations related to this gene include thiol-dependent ubiquitinyl hydrolase activity.

UniProtKB/Swiss-Prot for USP39 Gene

  • Plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the spliceosome. Regulates AURKB mRNA levels, and thereby plays a role in cytokinesis and in the spindle checkpoint. Does not have ubiquitin-specific peptidase activity, but could be a competitor of ubiquitin C-terminal hydrolases (UCHs).

Gene Wiki entry for USP39 Gene

Additional gene information for USP39 Gene

No data available for Entrez Gene Summary , CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for USP39 Gene

Genomics for USP39 Gene

GeneHancer (GH) Regulatory Elements for USP39 Gene

Promoters and enhancers for USP39 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH02J085615 Promoter/Enhancer 2.1 EPDnew Ensembl ENCODE 695.7 +13.8 13789 2.5 HDGF PKNOX1 SMAD1 ARNT ARID4B SIN3A DMAP1 ZNF2 YY1 POLR2B USP39 C2orf68 LOC100996506 LOC105374845 ELMOD3 SNORD94 GGCX GC02P085634
GH02J085600 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 685.2 +2.4 2445 8.7 FOXA2 MLX ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 KLF13 USP39 TMEM150A VAMP8 RETSAT C2orf68 LOC105374845 SNORD94 GGCX CAPG SH2D6
GH02J085536 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 79.9 -63.1 -63082 6.9 MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 ZNF143 GC02M085541 PIR39955 PIR40998 PARTICL MAT2A USP39 SNORD94 C2orf68 LOC100996506 KDM3A
GH02J086440 Promoter/Enhancer 2.4 EPDnew Ensembl ENCODE dbSUPER 31.6 +839.2 839183 3.6 CLOCK MLX ZFP64 FEZF1 DMAP1 IRF4 YY1 SLC30A9 ZNF213 E2F8 KDM3A GC02M086437 LOC102724642 SNORD94 C2orf68 ENSG00000231259 USP39 LOC100420889 LOC105374845 PTCD3
GH02J086193 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 32.8 +592.6 592606 3.9 ZFP64 DMAP1 YY1 SLC30A9 E2F8 ZNF143 SP3 NFYC SSRP1 ZNF610 IMMT GC02P086196 MRPL35 ENSG00000273080 LOC102724642 SNORD94 ENSG00000231259 LOC100420889 KDM3A USP39
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around USP39 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the USP39 gene promoter:
  • Nkx2-5
  • c-Jun
  • E47
  • Brachyury
  • AP-1
  • c-Fos
  • FosB
  • Fra-1
  • JunB
  • JunD

Genomic Locations for USP39 Gene

Genomic Locations for USP39 Gene
chr2:85,602,842-85,649,284
(GRCh38/hg38)
Size:
46,443 bases
Orientation:
Plus strand
chr2:85,829,979-85,876,406
(GRCh37/hg19)
Size:
46,428 bases
Orientation:
Plus strand

Genomic View for USP39 Gene

Genes around USP39 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
USP39 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for USP39 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for USP39 Gene

Proteins for USP39 Gene

  • Protein details for USP39 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Q53GS9-SNUT2_HUMAN
    Recommended name:
    U4/U6.U5 tri-snRNP-associated protein 2
    Protein Accession:
    Q53GS9
    Secondary Accessions:
    • A8K086
    • B3KM40
    • B4DHT4
    • D6W5L4
    • G5E9H0
    • Q6NX47
    • Q96RK9
    • Q9BV89
    • Q9H381
    • Q9P050
    • Q9Y310

    Protein attributes for USP39 Gene

    Size:
    565 amino acids
    Molecular mass:
    65381 Da
    Quaternary structure:
    • Component of the U4/U6-U5 tri-snRNP complex composed of the U4, U6 and U5 snRNAs and at least PRPF3, PRPF4, PRPF6, PRPF8, PRPF31, SNRNP200, TXNL4A, WDR57, SNRNP40, DDX23, CD2BP2, PPIH, SNU13, EFTUD2, SART1 and USP39.
    SequenceCaution:
    • Sequence=AAD27730.1; Type=Frameshift; Positions=Several; Evidence={ECO:0000305}; Sequence=AAG35521.1; Type=Erroneous initiation; Note=Translation N-terminally extended.; Evidence={ECO:0000305};

    Three dimensional structures from OCA and Proteopedia for USP39 Gene

    Alternative splice isoforms for USP39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP39 Gene

Post-translational modifications for USP39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for USP39 Gene

Domains & Families for USP39 Gene

Gene Families for USP39 Gene

Graphical View of Domain Structure for InterPro Entry

Q53GS9

UniProtKB/Swiss-Prot:

SNUT2_HUMAN :
  • Belongs to the peptidase C19 family.
Family:
  • Belongs to the peptidase C19 family.
genes like me logo Genes that share domains with USP39: view

Function for USP39 Gene

Molecular function for USP39 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in pre-mRNA splicing as a component of the U4/U6-U5 tri-snRNP, one of the building blocks of the spliceosome. Regulates AURKB mRNA levels, and thereby plays a role in cytokinesis and in the spindle checkpoint. Does not have ubiquitin-specific peptidase activity, but could be a competitor of ubiquitin C-terminal hydrolases (UCHs).

Phenotypes From GWAS Catalog for USP39 Gene

Gene Ontology (GO) - Molecular Function for USP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 17353931
GO:0008270 zinc ion binding IEA --
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with USP39: view
genes like me logo Genes that share phenotypes with USP39: view

Animal Models for USP39 Gene

MGI Knock Outs for USP39:
  • Usp39 Usp39<tm1b(EUCOMM)Hmgu>

Animal Model Products

  • Taconic Biosciences Mouse Models for USP39

miRNA for USP39 Gene

miRTarBase miRNAs that target USP39

Clone Products

  • Addgene plasmids for USP39

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for USP39 Gene

Localization for USP39 Gene

Subcellular locations from UniProtKB/Swiss-Prot for USP39 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for USP39 gene
Compartment Confidence
nucleus 5
cytosol 1

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for USP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm TAS --
GO:0005681 spliceosomal complex IEA --
genes like me logo Genes that share ontologies with USP39: view

Pathways & Interactions for USP39 Gene

genes like me logo Genes that share pathways with USP39: view

Pathways by source for USP39 Gene

Gene Ontology (GO) - Biological Process for USP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000245 spliceosomal complex assembly IEA --
GO:0000398 mRNA splicing, via spliceosome TAS --
GO:0006397 mRNA processing TAS 10022888
GO:0007049 cell cycle IEA --
GO:0008380 RNA splicing TAS 10022888
genes like me logo Genes that share ontologies with USP39: view

No data available for SIGNOR curated interactions for USP39 Gene

Drugs & Compounds for USP39 Gene

No Compound Related Data Available

Transcripts for USP39 Gene

Unigene Clusters for USP39 Gene

Ubiquitin specific peptidase 39:
Representative Sequences:

Clone Products

  • Addgene plasmids for USP39

Alternative Splicing Database (ASD) splice patterns (SP) for USP39 Gene

ExUns: 1a · 1b · 1c · 1d · 1e · 1f ^ 2 ^ 3 ^ 4a · 4b ^ 5a · 5b · 5c · 5d ^ 6 ^ 7 ^ 8 ^ 9 ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15a · 15b · 15c
SP1: - -
SP2: - -
SP3: - - -
SP4: -
SP5: - -
SP6: - -
SP7: -
SP8:
SP9: - -
SP10:

Relevant External Links for USP39 Gene

GeneLoc Exon Structure for
USP39
ECgene alternative splicing isoforms for
USP39

Expression for USP39 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for USP39 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

Protein differential expression in normal tissues from HIPED for USP39 Gene

This gene is overexpressed in Blymphocyte (9.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, MaxQB, and MOPED for USP39 Gene



Protein tissue co-expression partners for USP39 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of USP39 Gene:

USP39

SOURCE GeneReport for Unigene cluster for USP39 Gene:

Hs.654745

Evidence on tissue expression from TISSUES for USP39 Gene

  • Nervous system(4.7)
  • Skin(4.4)
  • Blood(4.3)
  • Liver(4.2)
  • Lung(2.5)
genes like me logo Genes that share expression patterns with USP39: view

No data available for mRNA differential expression in normal tissues , mRNA Expression by UniProt/SwissProt and Phenotype-based relationships between genes and organs from Gene ORGANizer for USP39 Gene

Orthologs for USP39 Gene

This gene was present in the common ancestor of eukaryotes.

Orthologs for USP39 Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia USP39 34 33
  • 99.71 (n)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP39 34
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USP39 34 33
  • 92.74 (n)
OneToOne
dog
(Canis familiaris)
Mammalia USP39 34 33
  • 92.39 (n)
OneToOne
oppossum
(Monodelphis domestica)
Mammalia USP39 34
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp39 33
  • 89.98 (n)
mouse
(Mus musculus)
Mammalia Usp39 16 34 33
  • 89.89 (n)
chicken
(Gallus gallus)
Aves USP39 34 33
  • 81.06 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP39 34
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp39 33
  • 78.41 (n)
Str.8201 33
zebrafish
(Danio rerio)
Actinopterygii usp39 34 33
  • 76.11 (n)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG7288 34 33
  • 62.87 (n)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008381 33
  • 62.66 (n)
worm
(Caenorhabditis elegans)
Secernentea F09D1.1 33
  • 57.79 (n)
usp-39 34
  • 52 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SAD1 36 34
  • 32 (a)
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G22350 33
  • 56.33 (n)
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3049 33
soybean
(Glycine max)
eudicotyledons Gma.6985 33
rice
(Oryza sativa)
Liliopsida Os09g0407900 33
  • 57.91 (n)
Os.7411 33
wheat
(Triticum aestivum)
Liliopsida Ta.9604 33
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1834 34
  • 61 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU09547 33
  • 54.86 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ubp10 33
  • 52.98 (n)
Species where no ortholog for USP39 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)

Evolution for USP39 Gene

ENSEMBL:
Gene Tree for USP39 (if available)
TreeFam:
Gene Tree for USP39 (if available)
Aminode:
Evolutionary constrained regions (ECRs) for USP39: view image

Paralogs for USP39 Gene

No data available for Paralogs for USP39 Gene

Variants for USP39 Gene

Sequence variations from dbSNP and Humsavar for USP39 Gene

SNP ID Clin Chr 02 pos Variation AA Info Type
rs1000033559 -- 85,605,076(+) A/G genic_upstream_transcript_variant, intron_variant
rs1000102395 -- 85,629,322(+) A/G intron_variant
rs1000106784 -- 85,605,460(+) T/C genic_upstream_transcript_variant, intron_variant
rs1000211109 -- 85,612,206(+) C/T 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, non_coding_transcript_variant
rs1000351466 -- 85,611,292(+) A/T genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant

Structural Variations from Database of Genomic Variants (DGV) for USP39 Gene

Variant ID Type Subtype PubMed ID
nsv215431 CNV deletion 16902084

Variation tolerance for USP39 Gene

Residual Variation Intolerance Score: 20.8% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 3.06; 50.60% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for USP39 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
USP39

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for USP39 Gene

Disorders for USP39 Gene

Additional Disease Information for USP39

Genetic Association Database
(GAD)
Human Genome Epidemiology Navigator
(HuGE)
ATLAS of Genetics and Cytogenetics in Oncology and Haematology

No disorders were found for USP39 Gene.

No data available for MalaCards , UniProtKB/Swiss-Prot and Genatlas for USP39 Gene

Publications for USP39 Gene

  1. Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score. (PMID: 20379614) Rose JE … Uhl GR (Molecular medicine (Cambridge, Mass.) 2010) 3 44 58
  2. Usp39 is essential for mitotic spindle checkpoint integrity and controls mRNA-levels of aurora B. (PMID: 18728397) van Leuken RJ … Medema RH (Cell cycle (Georgetown, Tex.) 2008) 3 4 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T … Sugano S (Nature genetics 2004) 3 4 58
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58

Products for USP39 Gene

  • Addgene plasmids for USP39

Sources for USP39 Gene

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