Human Gene SENP3 (ENST00000321337.12_4) from GENCODE V47lift37
  Description: SUMO specific peptidase 3 (from RefSeq NM_015670.6)
Gencode Transcript: ENST00000321337.12_4
Gencode Gene: ENSG00000161956.14_10
Transcript (Including UTRs)
   Position: hg19 chr17:7,465,236-7,475,287 Size: 10,052 Total Exon Count: 12 Strand: +
Coding Region
   Position: hg19 chr17:7,466,394-7,474,801 Size: 8,408 Coding Exon Count: 11 

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 (chr17:7,465,236-7,475,287)mRNA (may differ from genome)Protein (574 aa)
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-  Comments and Description Text from UniProtKB
  ID: SENP3_HUMAN
DESCRIPTION: RecName: Full=Sentrin-specific protease 3; EC=3.4.22.68; AltName: Full=SUMO-1-specific protease 3; AltName: Full=Sentrin/SUMO-specific protease SENP3;
FUNCTION: Protease that releases SUMO2 and SUMO3 monomers from sumoylated substrates, but has only weak activity against SUMO1 conjugates. Deconjugates SUMO2 from MEF2D, which increases its transcriptional activation capability. Deconjugates SUMO2 and SUMO3 from CDCA8. Redox sensor that, when redistributed into nucleoplasm, can act as an effector to enhance HIF1A transcriptional activity by desumoylating EP300. Required for rRNA processing through deconjugation of SUMO2 and SUMO3 from nucleophosmin, NPM1.
CATALYTIC ACTIVITY: Hydrolysis of the alpha-linked peptide bond in the sequence Gly-Gly-|-Ala-Thr-Tyr at the C-terminal end of the small ubiquitin-like modifier (SUMO) propeptide, Smt3, leading to the mature form of the protein. A second reaction involves the cleavage of an epsilon-linked peptide bond between the C-terminal glycine of the mature SUMO and the lysine epsilon-amino group of the target protein.
ENZYME REGULATION: On oxidative stress, SENP3 degradation is blocked by inhibition of its ubiquitination, which stabilizes it as it accumulates in the nucleoplasm.
SUBUNIT: Binds to SUMO1 and SUMO3 (By similarity). Component of some MLL1/MLL complex, at least composed of the core components MLL, ASH2L, HCFC1/HCF1, WDR5 and RBBP5, as well as the facultative components C17orf49, CHD8, E2F6, HSP70, INO80C, KANSL1, LAS1L, MAX, MCRS1, MGA, MYST1/MOF, PELP1, PHF20, PRP31, RING2, RUVB1/TIP49A, RUVB2/TIP49B, SENP3, TAF1, TAF4, TAF6, TAF7, TAF9 and TEX10. Interacts with EP300, NPM1 and CDCA8.
SUBCELLULAR LOCATION: Nucleus, nucleolus. Nucleus, nucleoplasm. Note=Redistributes between the nucleolus and the nucleoplasm in response to mild oxidative stress.
SIMILARITY: Belongs to the peptidase C48 family.

-  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

+  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: 30.14 RPKM in Testis
Total median expression: 964.47 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
5' UTR -171.80356-0.483 Picture PostScript Text
3' UTR -169.18486-0.348 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
IPR003653 - Peptidase_C48

Pfam Domains:
PF02902 - Ulp1 protease family, C-terminal catalytic domain
PF19722 - Sentrin-specific protease 3/5 N-terminal

SCOP Domains:
54001 - Cysteine proteinases

ModBase Predicted Comparative 3D Structure on Q9H4L4
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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 orthologNo orthologNo ortholog
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0004175 endopeptidase activity
GO:0005515 protein binding
GO:0008233 peptidase activity
GO:0008234 cysteine-type peptidase activity
GO:0016787 hydrolase activity

Biological Process:
GO:0006364 rRNA processing
GO:0006508 proteolysis
GO:0016926 protein desumoylation

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0071339 MLL1 complex


-  Descriptions from all associated GenBank mRNAs
  LF384758 - JP 2014500723-A/192261: Polycomb-Associated Non-Coding RNAs.
BC080658 - Homo sapiens SUMO1/sentrin/SMT3 specific peptidase 3, mRNA (cDNA clone MGC:90205 IMAGE:6155941), complete cds.
AL834294 - Homo sapiens mRNA; cDNA DKFZp762A152 (from clone DKFZp762A152).
AF199459 - Homo sapiens SUMO-1 specific protease 3 (SUSP3) mRNA, complete cds.
AY008763 - Homo sapiens sentrin/SUMO-specific protease (SENP3) mRNA, complete cds.
AB463293 - Synthetic construct DNA, clone: pF1KB8703, Homo sapiens SENP3 gene for SUMO1/sentrin/SMT3 specific peptidase 3, without stop codon, in Flexi system.
AM392699 - Synthetic construct Homo sapiens clone IMAGE:100002505 for hypothetical protein (SENP3 gene).
AM392708 - Synthetic construct Homo sapiens clone IMAGE:100002506 for hypothetical protein (SENP3 gene).
BC032613 - Homo sapiens cDNA clone IMAGE:5555330, **** WARNING: chimeric clone ****.
AL050283 - Homo sapiens mRNA; cDNA DKFZp586K0919 (from clone DKFZp586K0919).
BC048306 - Homo sapiens SUMO1/sentrin/SMT3 specific peptidase 3, mRNA (cDNA clone IMAGE:5554637), partial cds.
MA620335 - JP 2018138019-A/192261: Polycomb-Associated Non-Coding RNAs.
DL491810 - Novel nucleic acids.
DL490384 - Novel nucleic acids.
AK000923 - Homo sapiens cDNA FLJ10061 fis, clone HEMBA1001413.
JD020582 - Sequence 1606 from Patent EP1572962.
JD032437 - Sequence 13461 from Patent EP1572962.
JD022914 - Sequence 3938 from Patent EP1572962.
JD031543 - Sequence 12567 from Patent EP1572962.
JD031669 - Sequence 12693 from Patent EP1572962.
JD120945 - Sequence 101969 from Patent EP1572962.
JD434533 - Sequence 415557 from Patent EP1572962.
JD308024 - Sequence 289048 from Patent EP1572962.
JD251296 - Sequence 232320 from Patent EP1572962.
JD500493 - Sequence 481517 from Patent EP1572962.
JD281846 - Sequence 262870 from Patent EP1572962.
JD541689 - Sequence 522713 from Patent EP1572962.

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

Protein Q9H4L4 (Reactome details) participates in the following event(s):

R-HSA-6791226 Major pathway of rRNA processing in the nucleolus and cytosol
R-HSA-8868773 rRNA processing in the nucleus and cytosol
R-HSA-72312 rRNA processing
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000321337.1, ENST00000321337.10, ENST00000321337.11, ENST00000321337.2, ENST00000321337.3, ENST00000321337.4, ENST00000321337.5, ENST00000321337.6, ENST00000321337.7, ENST00000321337.8, ENST00000321337.9, NM_015670, Q66K15, Q86VS7, Q96PS4, Q9H4L4, Q9Y3W9, SENP3 , SENP3_HUMAN, SSP3, SUSP3, uc317raw.1, uc317raw.2
UCSC ID: ENST00000321337.12_4
RefSeq Accession: NM_015670.6
Protein: Q9H4L4 (aka SENP3_HUMAN or SEN3_HUMAN)

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