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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
  • 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

Summaries for USP39 Gene

GeneCards Summary for USP39 Gene

USP39 (Ubiquitin Specific Peptidase 39) is a Protein Coding gene. Among its related pathways are Gene Expression and mRNA Splicing - Major Pathway. 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

Promoters for USP39 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

ENSRs around USP39 on UCSC Golden Path with GeneCards custom track

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};

    Alternative splice isoforms for USP39 Gene

    UniProtKB/Swiss-Prot:

neXtProt entry for USP39 Gene

Proteomics data for USP39 Gene at MOPED

Post-translational modifications for USP39 Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

Antibody Products

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).
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

No data available for Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , 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
Jensen Localization Image for USP39 Gene COMPARTMENTS Subcellular localization image for USP39 gene
Compartment Confidence
nucleus 5
cytosol 1

No data available for Gene Ontology (GO) - Cellular Components for USP39 Gene

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:0006397 mRNA processing TAS 10022888
GO:0008380 RNA splicing TAS 10022888
GO:0016579 protein deubiquitination IEA --
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:

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 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, MOPED, and MaxQB for USP39 Gene



SOURCE GeneReport for Unigene cluster for USP39 Gene Hs.654745

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

Protein tissue co-expression partners for USP39 Gene

- Elite partner

Primer Products

In Situ Assay 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 36
  • 100 (a)
OneToOne
USP39 35
  • 99.71 (n)
  • 99.82 (a)
cow
(Bos Taurus)
Mammalia USP39 36
  • 98 (a)
OneToOne
USP39 35
  • 92.74 (n)
  • 97.88 (a)
dog
(Canis familiaris)
Mammalia USP39 35
  • 92.39 (n)
  • 98.75 (a)
USP39 36
  • 99 (a)
OneToOne
mouse
(Mus musculus)
Mammalia Usp39 36
  • 98 (a)
OneToOne
Usp39 16
Usp39 35
  • 89.89 (n)
  • 97.52 (a)
oppossum
(Monodelphis domestica)
Mammalia USP39 36
  • 92 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia USP39 36
  • 97 (a)
OneToOne
rat
(Rattus norvegicus)
Mammalia Usp39 35
  • 89.98 (n)
  • 97.09 (a)
chicken
(Gallus gallus)
Aves USP39 35
  • 81.06 (n)
  • 98.18 (a)
USP39 36
  • 90 (a)
OneToOne
lizard
(Anolis carolinensis)
Reptilia USP39 36
  • 97 (a)
OneToOne
tropical clawed frog
(Silurana tropicalis)
Amphibia Str.8201 35
usp39 35
  • 78.41 (n)
  • 91.09 (a)
zebrafish
(Danio rerio)
Actinopterygii usp39 35
  • 76.11 (n)
  • 88.5 (a)
usp39 36
  • 87 (a)
OneToOne
African malaria mosquito
(Anopheles gambiae)
Insecta AgaP_AGAP008381 35
  • 62.66 (n)
  • 63.33 (a)
fruit fly
(Drosophila melanogaster)
Insecta CG7288 35
  • 62.87 (n)
  • 64.99 (a)
CG7288 36
  • 62 (a)
OneToOne
worm
(Caenorhabditis elegans)
Secernentea usp-39 36
  • 52 (a)
OneToOne
F09D1.1 35
  • 57.79 (n)
  • 58.72 (a)
baker's yeast
(Saccharomyces cerevisiae)
Saccharomycetes SAD1 36
  • 32 (a)
OneToOne
SAD1 38
Alicante grape
(Vitis vinifera)
eudicotyledons Vvi.3049 35
soybean
(Glycine max)
eudicotyledons Gma.6985 35
thale cress
(Arabidopsis thaliana)
eudicotyledons AT4G22350 35
  • 56.33 (n)
  • 51.53 (a)
rice
(Oryza sativa)
Liliopsida Os.7411 35
Os09g0407900 35
  • 57.91 (n)
  • 53.6 (a)
wheat
(Triticum aestivum)
Liliopsida Ta.9604 35
bread mold
(Neurospora crassa)
Ascomycetes NCU09547 35
  • 54.86 (n)
  • 49.24 (a)
fission yeast
(Schizosaccharomyces pombe)
Schizosaccharomycetes ubp10 35
  • 52.98 (n)
  • 50.35 (a)
sea squirt
(Ciona savignyi)
Ascidiacea CSA.1834 36
  • 61 (a)
OneToOne
Species with no ortholog for USP39:
  • 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
rs9805 -- 85,649,077(-) TGGAG(A/G)AGGGT nc-transcript-variant, utr-variant-3-prime
rs1000358 -- 85,620,926(-) ATACC(C/T)ATAAA intron-variant
rs1000359 -- 85,620,579(-) taaaa(C/T)ttaaa intron-variant
rs3821020 -- 85,642,799(+) TTTGT(C/T)GGAGA intron-variant
rs3832098 -- 85,649,102(+) ATGTC(-/T)TGAGT nc-transcript-variant, utr-variant-3-prime

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

Variant ID Type Subtype PubMed ID
dgv4202n71 CNV Loss 21882294
nsv215431 CNV Loss 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

HapMap Linkage Disequilibrium report
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 48 67
  2. Human and mouse proteases: a comparative genomic approach. (PMID: 12838346) Puente X.S. … Lopez-Otin C. (Nat. Rev. Genet. 2003) 2 3
  3. Temporal proteomics of NGF-TrkA signaling identifies an inhibitory role for the E3 ligase Cbl-b in neuroblastoma cell differentiation. (PMID: 25921289) Emdal K.B. … Olsen J.V. (Sci Signal 2015) 3
  4. Panorama of ancient metazoan macromolecular complexes. (PMID: 26344197) Wan C. … Emili A. (Nature 2015) 3
  5. Characterizing WW domain interactions of tumor suppressor WWOX reveals its association with multiprotein networks. (PMID: 24550385) Abu-Odeh M. … Aqeilan R.I. (J. Biol. Chem. 2014) 3

Products for USP39 Gene

Sources for USP39 Gene

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