Human Gene USP39 (ENST00000323701.11_5) from GENCODE V47lift37
  Description: ubiquitin specific peptidase 39, transcript variant 1 (from RefSeq NM_006590.4)
Gencode Transcript: ENST00000323701.11_5
Gencode Gene: ENSG00000168883.20_14
Transcript (Including UTRs)
   Position: hg19 chr2:85,843,309-85,876,406 Size: 33,098 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr2:85,843,319-85,875,931 Size: 32,613 Coding Exon Count: 13 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr2:85,843,309-85,876,406)mRNA (may differ from genome)Protein (565 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsHGNC
MGIOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SNUT2_HUMAN
DESCRIPTION: RecName: Full=U4/U6.U5 tri-snRNP-associated protein 2; AltName: Full=Inactive ubiquitin-specific peptidase 39; AltName: Full=SAD1 homolog; AltName: Full=U4/U6.U5 tri-snRNP-associated 65 kDa protein; Short=65K;
FUNCTION: May play a role in mRNA splicing. It is unsure if the protein really exhibits hydrolase activity. Could be a competitor of ubiquitin C-terminal hydrolases (UCHs).
SUBUNIT: Part of a tri-snRNP complex.
SUBCELLULAR LOCATION: Nucleus.
SIMILARITY: Belongs to the peptidase C19 family.
SIMILARITY: Contains 1 UBP-type zinc finger.
SEQUENCE CAUTION: Sequence=AAD27730.1; Type=Frameshift; Positions=Several; Sequence=AAG35521.1; Type=Erroneous initiation;

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 17.32 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 600.88 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
3' UTR -147.00475-0.309 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001394 - Peptidase_C19
IPR015880 - Znf_C2H2-like
IPR013083 - Znf_RING/FYVE/PHD
IPR001607 - Znf_UBP

Pfam Domains:
PF00443 - Ubiquitin carboxyl-terminal hydrolase
PF02148 - Zn-finger in ubiquitin-hydrolases and other protein

SCOP Domains:
54001 - Cysteine proteinases
57850 - RING/U-box

ModBase Predicted Comparative 3D Structure on Q53GS9
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologGenome BrowserGenome Browser
Gene DetailsGene Details Gene DetailsGene DetailsGene Details
Gene SorterGene Sorter Gene SorterGene SorterGene Sorter
 RGDEnsembl WormBaseSGD
    Protein SequenceProtein Sequence
    AlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0008270 zinc ion binding
GO:0036459 thiol-dependent ubiquitinyl hydrolase activity
GO:0046872 metal ion binding

Biological Process:
GO:0000245 spliceosomal complex assembly
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0007049 cell cycle
GO:0008380 RNA splicing
GO:0016579 protein deubiquitination
GO:0051301 cell division

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005681 spliceosomal complex


-  Descriptions from all associated GenBank mRNAs
  AK056334 - Homo sapiens cDNA FLJ31772 fis, clone NT2RI2008007, highly similar to U4/U6.U5 tri-snRNP-associated protein 2.
AK295257 - Homo sapiens cDNA FLJ59519 complete cds, highly similar to U4/U6.U5 tri-snRNP-associated protein 2.
AK302236 - Homo sapiens cDNA FLJ56173 complete cds, highly similar to U4/U6.U5 tri-snRNP-associated protein 2.
AK289451 - Homo sapiens cDNA FLJ75565 complete cds, highly similar to Homo sapiens ubiquitin specific peptidase 39 (USP39), mRNA.
AK129872 - Homo sapiens cDNA FLJ26362 fis, clone HRT05326, highly similar to Homo sapiens CGI-21 protein mRNA.
BC067273 - Homo sapiens ubiquitin specific peptidase 39, mRNA (cDNA clone MGC:75069 IMAGE:6503509), complete cds.
AF353989 - Homo sapiens U4/U6.U5 tri-snRNP-associated 65 kDa protein mRNA, complete cds.
AF132955 - Homo sapiens CGI-21 protein mRNA, complete cds.
AK222852 - Homo sapiens mRNA for ubiquitin specific protease 39 variant, clone: HEP08452.
AK001047 - Homo sapiens cDNA FLJ10185 fis, clone HEMBA1004509, highly similar to U4/U6.U5 tri-snRNP-associated protein 2.
CU688266 - Synthetic construct Homo sapiens gateway clone IMAGE:100022840 5' read USP39 mRNA.
KJ893118 - Synthetic construct Homo sapiens clone ccsbBroadEn_02512 USP39 gene, encodes complete protein.
BC001384 - Homo sapiens ubiquitin specific peptidase 39, mRNA (cDNA clone IMAGE:3050936), partial cds.
AK309485 - Homo sapiens cDNA, FLJ99526.
AF130096 - Homo sapiens clone FLC0586 PRO2855 mRNA, complete cds.
AL117416 - Homo sapiens mRNA; cDNA DKFZp566I0947 (from clone DKFZp566I0947).
JD524155 - Sequence 505179 from Patent EP1572962.
JD223878 - Sequence 204902 from Patent EP1572962.
JD411392 - Sequence 392416 from Patent EP1572962.
JD320458 - Sequence 301482 from Patent EP1572962.
AK001772 - Homo sapiens cDNA FLJ10910 fis, clone OVARC1000139, highly similar to U4/U6.U5 tri-snRNP-associated protein 2.
AF161450 - Homo sapiens HSPC332 mRNA, partial cds.
JD229808 - Sequence 210832 from Patent EP1572962.
AK057698 - Homo sapiens cDNA FLJ33136 fis, clone UTERU1000065.
JD248306 - Sequence 229330 from Patent EP1572962.
JD381107 - Sequence 362131 from Patent EP1572962.
JD364046 - Sequence 345070 from Patent EP1572962.
JD449495 - Sequence 430519 from Patent EP1572962.
JD091857 - Sequence 72881 from Patent EP1572962.
JD303614 - Sequence 284638 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q53GS9 (Reactome details) participates in the following event(s):

R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A8K086, B3KM40, B4DHT4, CGI-21, D6W5L4, ENST00000323701.1, ENST00000323701.10, ENST00000323701.2, ENST00000323701.3, ENST00000323701.4, ENST00000323701.5, ENST00000323701.6, ENST00000323701.7, ENST00000323701.8, ENST00000323701.9, G5E9H0, HSPC332, NM_006590, PRO2855, Q53GS9, Q6NX47, Q96RK9, Q9BV89, Q9H381, Q9P050, Q9Y310, UBP39_HUMAN, uc317rnc.1, uc317rnc.2, USP39
UCSC ID: ENST00000323701.11_5
RefSeq Accession: NM_006590.4
Protein: Q53GS9 (aka SNUT2_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.