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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
  • SNRNP65 3
  • HSPC332 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

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. 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

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

Genomics for USP39 Gene

Regulatory Elements for USP39 Gene

Enhancers for USP39 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH02F085497 1.7 FANTOM5 Ensembl ENCODE 23.9 -100.1 -100068 10.5 HDGF ARNT MLX ARID4B SIN3A DMAP1 YY1 ZNF143 FOS KLF13 USP39 TMEM150A TCF7L1 MAT2A SNORD94 LOC100996506 RN7SL251P RNU7-64P CAPG C2orf68
GH02F085615 1.1 ENCODE 33.8 +13.8 13790 2.5 HDGF PKNOX1 ARNT CREB3L1 ARID4B SIN3A DMAP1 ZNF2 YY1 CBX5 USP39 C2orf68 SNORD94 TCF7L1 MAT2A GGCX GC02P085634
GH02F085600 1.1 ENCODE 25.3 +2.4 2445 8.7 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 KLF13 USP39 TCF7L1 VAMP8 RETSAT TMEM150A GGCX CAPG SH2D6 RNU1-38P ATOH8
GH02F085594 1.1 ENCODE 24.7 -7.0 -6952 3.7 HDGF PKNOX1 ATF1 ARID4B SIN3A ZNF48 ZNF2 ETS1 YY1 ELK1 USP39 VAMP8 GGCX RNF181 VAMP5 GC02M085595
GH02F085550 1.2 Ensembl ENCODE 19.5 -52.4 -52351 4.0 ELF3 HDGF PKNOX1 ARID4B SIN3A ZNF48 DNMT3B RAD21 RFX5 RARA USP39 GGCX VAMP8 CAPG SH2D6 TGOLN2 TMEM150A RN7SL251P RNU7-64P RETSAT
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around USP39 on UCSC Golden Path with GeneCards custom track

Promoters for USP39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters
ENSR00000593754 58 2201 CREB3L1 MLX ARID4B SIN3A DMAP1 YY1 ZNF766 ZNF207 ZNF143 KLF13

Genomic Location for USP39 Gene

Chromosome:
2
Start:
85,602,842 bp from pter
End:
85,649,284 bp from pter
Size:
46,443 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 :
  • Contains 1 USP domain.
  • Belongs to the peptidase C19 family.
  • Contains 1 UBP-type zinc finger.
Domain:
  • Contains 1 USP domain.
Family:
  • Belongs to the peptidase C19 family.
Similarity:
  • Contains 1 UBP-type zinc finger.
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).

Gene Ontology (GO) - Molecular Function for USP39 Gene

GO ID Qualified GO term Evidence PubMed IDs
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:

Animal Model Products

  • Taconic Biosciences Mouse Models for USP39

miRNA for USP39 Gene

miRTarBase miRNAs that target USP39

Inhibitory RNA Products

Flow Cytometry Products

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

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

Transcripts for USP39 Gene

Unigene Clusters for USP39 Gene

Ubiquitin specific peptidase 39:
Representative Sequences:

Inhibitory RNA Products

Flow Cytometry Products

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 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, PaxDb, 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
genes like me logo Genes that share expression patterns with USP39: view

Primer Products

No data available for mRNA differential expression in normal tissues and mRNA Expression by UniProt/SwissProt 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 35
  • 99.71 (n)
platypus
(Ornithorhynchus anatinus)
Mammalia USP39 35
  • 97 (a)
OneToOne
cow
(Bos Taurus)
Mammalia USP39 34 35
  • 92.74 (n)
dog
(Canis familiaris)
Mammalia USP39 34 35
  • 92.39 (n)
oppossum
(Monodelphis domestica)
Mammalia USP39 35
  • 92 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp39 34
  • 89.98 (n)
mouse
(Mus musculus)
Mammalia Usp39 34 16 35
  • 89.89 (n)
chicken
(Gallus gallus)
Aves USP39 34 35
  • 81.06 (n)
lizard
(Anolis carolinensis)
Reptilia USP39 35
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia usp39 34
  • 78.41 (n)
Str.8201 34
zebrafish
(Danio rerio)
Actinopterygii usp39 34 35
  • 76.11 (n)
fruit fly
(Drosophila melanogaster)
Insecta CG7288 34 35
  • 62.87 (n)
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008381 34
  • 62.66 (n)
worm
(Caenorhabditis elegans)
Secernentea F09D1.1 34
  • 57.79 (n)
usp-39 35
  • 52 (a)
OneToOne
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SAD1 35 37
  • 32 (a)
OneToOne
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G22350 34
  • 56.33 (n)
soybean
(Glycine max)
eudicotyledons Gma.6985 34
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3049 34
rice
(Oryza sativa)
Liliopsida Os09g0407900 34
  • 57.91 (n)
Os.7411 34
wheat
(Triticum aestivum)
Liliopsida Ta.9604 34
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1834 35
  • 61 (a)
OneToOne
bread mold
(Neurospora crassa)
Ascomycetes NCU09547 34
  • 54.86 (n)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ubp10 34
  • 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)

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 Sequence Context AA Info Type
rs1000358 -- 85,620,926(-) ATACC(C/T)ATAAA intron-variant
rs1000359 -- 85,620,579(-) taaaa(C/T)ttaaa intron-variant
rs10170768 -- 85,608,742(+) AGAAT(A/T)TCAGG intron-variant, utr-variant-3-prime
rs10180770 -- 85,641,926(+) AAAAA(A/G)AAAGA intron-variant
rs10181854 -- 85,629,643(+) aggcg(C/T)gtgcc intron-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)

Relevant External Links for USP39 Gene

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

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

Disorders for USP39 Gene

Relevant External Links for USP39

Genetic Association Database (GAD)
USP39
Human Genome Epidemiology (HuGE) Navigator
USP39
Atlas of Genetics and Cytogenetics in Oncology and Haematology:
USP39

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 J.E. … Uhl G.R. (Mol. Med. 2010) 3 46 64
  2. Usp39 is essential for mitotic spindle checkpoint integrity and controls mRNA-levels of aurora B. (PMID: 18728397) van Leuken R.J. … Medema R.H. (Cell Cycle 2008) 3 4 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  4. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PMID: 14702039) Ota T. … Sugano S. (Nat. Genet. 2004) 3 4 64
  5. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64

Products for USP39 Gene

Sources for USP39 Gene

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