Human Gene SENP2 (ENST00000296257.10) from GENCODE V44
  Description: Homo sapiens SUMO specific peptidase 2 (SENP2), mRNA. (from RefSeq NM_021627)
RefSeq Summary (NM_021627): SUMO1 (UBL1; MIM 601912) is a small ubiquitin-like protein that can be covalently conjugated to other proteins. SENP2 is one of a group of enzymes that process newly synthesized SUMO1 into the conjugatable form and catalyze the deconjugation of SUMO1-containing species.[supplied by OMIM, Apr 2004].
Gencode Transcript: ENST00000296257.10
Gencode Gene: ENSG00000163904.13
Transcript (Including UTRs)
   Position: hg38 chr3:185,586,295-185,633,551 Size: 47,257 Total Exon Count: 17 Strand: +
Coding Region
   Position: hg38 chr3:185,586,414-185,629,844 Size: 43,431 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersCTDRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr3:185,586,295-185,633,551)mRNA (may differ from genome)Protein (589 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeUniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: SENP2_HUMAN
DESCRIPTION: RecName: Full=Sentrin-specific protease 2; EC=3.4.22.68; AltName: Full=Axam2; AltName: Full=SMT3-specific isopeptidase 2; Short=Smt3ip2; AltName: Full=Sentrin/SUMO-specific protease SENP2;
FUNCTION: Protease that catalyzes two essential functions in the SUMO pathway: processing of full-length SUMO1, SUMO2 and SUMO3 to their mature forms and deconjugation of SUMO1, SUMO2 and SUMO3 from targeted proteins. May down-regulate CTNNB1 levels and thereby modulate the Wnt pathway (By similarity).
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.
SUBUNIT: Binds to SUMO2 and SUMO3 (By similarity). Interacts with the C-terminal domain of NUP153 via its N-terminus.
INTERACTION: Q9Y6K9:IKBKG; NbExp=3; IntAct=EBI-714881, EBI-81279;
SUBCELLULAR LOCATION: Nucleus, nuclear pore complex. Nucleus membrane; Peripheral membrane protein; Nucleoplasmic side. Cytoplasm. Note=Shuttles between cytoplasm and nucleus.
DOMAIN: The N-terminus is necessary and sufficient for nuclear envelope targeting.
PTM: Polyubiquitinated; which leads to proteasomal degradation.
SIMILARITY: Belongs to the peptidase C48 family.

-  Primer design for this transcript
 

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 22.42 RPKM in Testis
Total median expression: 387.01 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -67.60119-0.568 Picture PostScript Text
3' UTR -1093.403707-0.295 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

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1TGZ - X-ray MuPIT 1TH0 - X-ray MuPIT 2IO0 - X-ray MuPIT 2IO1 - X-ray MuPIT 2IO2 - X-ray MuPIT 2IO3 - X-ray MuPIT


ModBase Predicted Comparative 3D Structure on Q9HC62
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-  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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  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
GO:0019904 protein domain specific binding
GO:0070139 SUMO-specific endopeptidase activity
GO:0070140 SUMO-specific isopeptidase activity

Biological Process:
GO:0001934 positive regulation of protein phosphorylation
GO:0006508 proteolysis
GO:0007507 heart development
GO:0009950 dorsal/ventral axis specification
GO:0015031 protein transport
GO:0016055 Wnt signaling pathway
GO:0016925 protein sumoylation
GO:0016926 protein desumoylation
GO:0030111 regulation of Wnt signaling pathway
GO:0031397 negative regulation of protein ubiquitination
GO:0031398 positive regulation of protein ubiquitination
GO:0031648 protein destabilization
GO:0032091 negative regulation of protein binding
GO:0032875 regulation of DNA endoreduplication
GO:0035562 negative regulation of chromatin binding
GO:0043518 negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0045444 fat cell differentiation
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0051028 mRNA transport
GO:0051246 regulation of protein metabolic process
GO:0060707 trophoblast giant cell differentiation
GO:0060711 labyrinthine layer development
GO:0060712 spongiotrophoblast layer development
GO:1901797 negative regulation of signal transduction by p53 class mediator
GO:2000045 regulation of G1/S transition of mitotic cell cycle

Cellular Component:
GO:0005634 nucleus
GO:0005643 nuclear pore
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0016020 membrane
GO:0016604 nuclear body
GO:0016605 PML body
GO:0031410 cytoplasmic vesicle
GO:0031965 nuclear membrane


-  Descriptions from all associated GenBank mRNAs
  KJ894484 - Synthetic construct Homo sapiens clone ccsbBroadEn_03878 SENP2 gene, encodes complete protein.
AK298628 - Homo sapiens cDNA FLJ56470 complete cds, highly similar to Sentrin-specific protease 2 (EC 3.4.22.-).
AK304402 - Homo sapiens cDNA FLJ54905 complete cds, highly similar to Sentrin-specific protease 2 (EC 3.4.22.-).
AF151697 - Homo sapiens sentrin-specific protease (SENP2) mRNA, complete cds.
AK296772 - Homo sapiens cDNA FLJ61308 complete cds, highly similar to Sentrin-specific protease 2 (EC 3.4.22.-).
AK027599 - Homo sapiens cDNA FLJ14693 fis, clone NT2RP2005360, weakly similar to Homo sapiens sentrin/SUMO-specific protease (SENP1) mRNA.
AK296744 - Homo sapiens cDNA FLJ60649 complete cds, highly similar to Sentrin-specific protease 2 (EC 3.4.22.-).
BC040609 - Homo sapiens SUMO1/sentrin/SMT3 specific peptidase 2, mRNA (cDNA clone MGC:49871 IMAGE:5163937), complete cds.
CU691906 - Synthetic construct Homo sapiens gateway clone IMAGE:100021431 5' read SENP2 mRNA.
AB385449 - Synthetic construct DNA, clone: pF1KA1331, Homo sapiens SENP2 gene for sentrin-specific protease 2, complete cds, without stop codon, in Flexi system.
AB037752 - Homo sapiens KIAA1331 mRNA for KIAA1331 protein.
AL834380 - Homo sapiens mRNA; cDNA DKFZp762A2316 (from clone DKFZp762A2316).
JD476128 - Sequence 457152 from Patent EP1572962.
AK074357 - Homo sapiens cDNA FLJ23777 fis, clone HEP20690, highly similar to Homo sapiens sentrin-specific protease (SENP2) mRNA.
LF210584 - JP 2014500723-A/18087: Polycomb-Associated Non-Coding RNAs.
MA446161 - JP 2018138019-A/18087: Polycomb-Associated Non-Coding RNAs.
LF338901 - JP 2014500723-A/146404: Polycomb-Associated Non-Coding RNAs.
MA574478 - JP 2018138019-A/146404: Polycomb-Associated Non-Coding RNAs.
JD037630 - Sequence 18654 from Patent EP1572962.
JD565131 - Sequence 546155 from Patent EP1572962.
JD417881 - Sequence 398905 from Patent EP1572962.
LF338900 - JP 2014500723-A/146403: Polycomb-Associated Non-Coding RNAs.
MA574477 - JP 2018138019-A/146403: Polycomb-Associated Non-Coding RNAs.
JD160656 - Sequence 141680 from Patent EP1572962.
BC018020 - Homo sapiens SUMO1/sentrin/SMT3 specific peptidase 2, mRNA (cDNA clone IMAGE:4286856).
JD256280 - Sequence 237304 from Patent EP1572962.
JD551000 - Sequence 532024 from Patent EP1572962.
JD357567 - Sequence 338591 from Patent EP1572962.
JD564110 - Sequence 545134 from Patent EP1572962.
JD436321 - Sequence 417345 from Patent EP1572962.
JD153264 - Sequence 134288 from Patent EP1572962.
JD457429 - Sequence 438453 from Patent EP1572962.
JD415020 - Sequence 396044 from Patent EP1572962.
JD415021 - Sequence 396045 from Patent EP1572962.
JD120604 - Sequence 101628 from Patent EP1572962.
JD379770 - Sequence 360794 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04310 - Wnt signaling pathway

Reactome (by CSHL, EBI, and GO)

Protein Q9HC62 (Reactome details) participates in the following event(s):

R-HSA-2990840 SENP1,2,5 proteolytically process SUMO1
R-HSA-2990842 SEN1,2,5 proteolytically process SUMO2
R-HSA-2993763 SENP1,2,5 proteolytically process SUMO3
R-HSA-3065679 SUMO is proteolytically processed
R-HSA-3215018 Processing and activation of SUMO
R-HSA-2990846 SUMOylation
R-HSA-597592 Post-translational protein modification
R-HSA-392499 Metabolism of proteins

-  Other Names for This Gene
  Alternate Gene Symbols: ENST00000296257.1, ENST00000296257.2, ENST00000296257.3, ENST00000296257.4, ENST00000296257.5, ENST00000296257.6, ENST00000296257.7, ENST00000296257.8, ENST00000296257.9, KIAA1331, NM_021627, Q8IW97, Q96SR2, Q9HC62, Q9P2L5, SENP2_HUMAN, uc003fpn.1, uc003fpn.2, uc003fpn.3, uc003fpn.4, uc003fpn.5
UCSC ID: ENST00000296257.10
RefSeq Accession: NM_021627
Protein: Q9HC62 (aka SENP2_HUMAN or SNP2_HUMAN)
CCDS: CCDS33902.1

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