SENP3
SUMO specific peptidase 3 | DKFZP586K0919, DKFZp762A152, SMT3IP1, SSP3, Ulp1

The reversible posttranslational modification of proteins by the addition of small ubiquitin-like SUMO proteins (see SUMO1; MIM 601912) is required for numerous biologic processes. SUMO-specific proteases, such as SENP3, are responsible for the initial processing of SUMO precursors to generate a C-terminal diglycine motif required for the conjugation reaction. They also have isopeptidase activity for the removal of SUMO from high molecular mass SUMO conjugates (Di Bacco et al., 2006 [PubMed 16738315]).[supplied by OMIM, Jun 2009]

Member of: DE-5 DE-5.24
Biological processes 22 terms
MLL1 complex (GO:0071339)cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA) (GO:0000448)cysteine-type deubiquitinase activity (GO:0004843)cysteine-type peptidase activity (GO:0008234)cysteine-type peptidase activity (GO:0008234)cytoplasm (GO:0005737)deSUMOylase activity (GO:0016929)deSUMOylase activity (GO:0016929)deSUMOylase activity (GO:0016929)negative regulation of double-strand break repair via homologous recombination (GO:2000042)nucleolus (GO:0005730)nucleolus (GO:0005730)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleoplasm (GO:0005654)nucleus (GO:0005634)nucleus (GO:0005634)protein binding (GO:0005515)protein desumoylation (GO:0016926)protein desumoylation (GO:0016926)protein desumoylation (GO:0016926)proteolysis (GO:0006508)
Expression (TPM)
SENP3 — as a Regulated Gene

TFs regulating SENP3 0 TFs

Transcription factors with Perturb-seq knockdown data for SENP3. The Binding column indicates whether any binding evidence exists for this TF–gene pair (ChIP-seq or motif footprint peaks). The Mean coef is the average Perturb-seq regression coefficient across active gRNAs (positive = SENP3 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to SENP3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of SENP3, linked by TSS proximity or chromatin conformation (Multiome / HiCAR). Each element overlaps at least one TF ChIP-seq binding site — the TFs column shows how many distinct TFs bind that element.

Accessibility Element Dist. to TSS Link type TFs
chr17:7,260,746–7,263,748 299.3 kb Distal (>10kb) Multiome 639
chr17:7,280,161–7,282,555 280.2 kb Distal (>10kb) Multiome 841
chr17:7,293,901–7,295,189 267.2 kb Distal (>10kb) Multiome 443
chr17:7,296,224–7,296,683 265.3 kb Distal (>10kb) Multiome 688
chr17:7,306,788–7,309,027 254.5 kb Distal (>10kb) Multiome 896
chr17:7,314,722–7,315,725 246.6 kb Distal (>10kb) Multiome 843
chr17:7,328,881–7,330,972 232.4 kb Distal (>10kb) Multiome 809
chr17:7,349,378–7,350,590 211.7 kb Distal (>10kb) Multiome 414
chr17:7,351,208–7,352,575 209.9 kb Distal (>10kb) Multiome 857
chr17:7,356,082–7,356,523 205.7 kb Distal (>10kb) Multiome 485
chr17:7,383,791–7,384,537 177.7 kb Distal (>10kb) Multiome 218
chr17:7,393,924–7,395,223 167.2 kb Distal (>10kb) Multiome HiCAR 744
chr17:7,403,290–7,405,695 157.6 kb Distal (>10kb) Multiome 838
chr17:7,435,167–7,437,681 124.8 kb Distal (>10kb) Multiome HiCAR 828
chr17:7,437,892–7,438,555 123.6 kb Distal (>10kb) Multiome HiCAR 224
chr17:7,440,048–7,441,211 121.2 kb Distal (>10kb) Multiome 487
chr17:7,444,968–7,446,142 116.3 kb Distal (>10kb) Multiome 632
chr17:7,455,450–7,456,019 106.3 kb Distal (>10kb) Multiome 414
chr17:7,478,839–7,480,126 82.4 kb Distal (>10kb) Multiome 574
chr17:7,483,139–7,485,576 77.5 kb Distal (>10kb) Multiome 1156
chr17:7,548,693–7,549,285 12.9 kb Distal (>10kb) Multiome 387
chr17:7,557,954–7,558,343 3.6 kb Proximal (<10kb) 431
chr17:7,560,249–7,562,536 22 bp At TSS Multiome 759
chr17:7,572,039–7,574,418 12.0 kb Distal (>10kb) Multiome 1071
chr17:7,579,018–7,579,876 17.5 kb Distal (>10kb) Multiome 844
chr17:7,583,063–7,584,547 21.9 kb Distal (>10kb) Multiome 921
chr17:7,588,871–7,590,534 28.2 kb Distal (>10kb) Multiome 319
chr17:7,614,065–7,615,780 53.2 kb Distal (>10kb) Multiome 708
chr17:7,627,090–7,628,247 65.9 kb Distal (>10kb) Multiome 712
chr17:7,650,010–7,652,127 88.9 kb Distal (>10kb) Multiome 467
chr17:7,685,876–7,686,907 124.4 kb Distal (>10kb) Multiome 765
chr17:7,687,214–7,687,777 125.6 kb Distal (>10kb) Multiome 710
chr17:7,687,867–7,688,863 126.4 kb Distal (>10kb) Multiome 700
chr17:7,703,383–7,703,975 141.7 kb Distal (>10kb) Multiome 141
chr17:7,704,799–7,705,590 143.2 kb Distal (>10kb) Multiome 325
chr17:7,716,832–7,717,983 155.4 kb Distal (>10kb) Multiome 759
chr17:7,833,417–7,837,960 273.7 kb Distal (>10kb) Multiome 1160
chr17:7,841,438–7,843,228 280.3 kb Distal (>10kb) Multiome 861
chr17:7,843,355–7,844,130 281.7 kb Distal (>10kb) Multiome 614
chr17:7,844,349–7,845,186 283.0 kb Distal (>10kb) Multiome 617
chr17:7,851,538–7,852,239 289.9 kb Distal (>10kb) Multiome 531
chr17:7,856,600–7,858,747 295.6 kb Distal (>10kb) Multiome 942

Genome Browser

Genomic view of the SENP3 locus showing ATAC-seq accessibility and RNA-seq expression across the ESC → DE time course, together with TF binding peaks and element-to-TSS loop connections.

chr17:7,250,746 – 7,868,747
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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