Predicted to enable cysteine-type deubiquitinase activity and zinc ion binding activity. Involved in spliceosomal complex assembly. Located in nucleoplasm. Part of U4/U6 x U5 tri-snRNP complex. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for USP39. 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 = USP39 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.
| TF | Mean coef | Binding | Outlier | TF→Gene link |
|---|
Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of USP39, 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 |
|---|---|---|---|---|
| chr2:85,327,503–85,328,538 | 274.8 kb | Distal (>10kb) Multiome | 1009 | |
| chr2:85,354,014–85,355,224 | 248.2 kb | Distal (>10kb) Multiome | 962 | |
| chr2:85,413,587–85,414,333 | 189.0 kb | Distal (>10kb) Multiome | 351 | |
| chr2:85,418,133–85,419,210 | 184.3 kb | Distal (>10kb) Multiome | 885 | |
| chr2:85,420,473–85,421,406 | 182.0 kb | Distal (>10kb) Multiome | 853 | |
| chr2:85,437,445–85,438,463 | 165.0 kb | Distal (>10kb) Multiome | 501 | |
| chr2:85,455,501–85,456,436 | 146.9 kb | Distal (>10kb) Multiome | 268 | |
| chr2:85,468,626–85,469,195 | 134.0 kb | Distal (>10kb) Multiome | 496 | |
| chr2:85,537,623–85,540,152 | 65.1 kb | Distal (>10kb) Multiome | 1210 | |
| chr2:85,546,252–85,547,149 | 56.4 kb | Distal (>10kb) Multiome | 418 | |
| chr2:85,561,042–85,561,982 | 41.3 kb | Distal (>10kb) Multiome | 903 | |
| chr2:85,577,411–85,578,045 | 25.3 kb | Distal (>10kb) Multiome | 505 | |
| chr2:85,578,935–85,580,041 | 23.2 kb | Distal (>10kb) Multiome | 275 | |
| chr2:85,584,249–85,584,853 | 18.3 kb | Distal (>10kb) Multiome | 633 | |
| chr2:85,595,068–85,596,226 | 7.2 kb | Proximal (<10kb) Multiome | 804 | |
| chr2:85,601,954–85,603,493 | 146 bp | At TSS Multiome | 852 | |
| chr2:85,611,558–85,612,589 | 9.2 kb | Proximal (<10kb) Multiome | 875 | |
| chr2:85,615,831–85,616,609 | 13.3 kb | Distal (>10kb) Multiome | 898 | |
| chr2:85,678,904–85,679,599 | 76.5 kb | Distal (>10kb) Multiome | 445 | |
| chr2:85,753,145–85,755,032 | 151.0 kb | Distal (>10kb) Multiome | 527 | |
| chr2:85,827,451–85,827,914 | 224.8 kb | Distal (>10kb) Multiome | 364 | |
| chr2:85,888,294–85,889,666 | 286.2 kb | Distal (>10kb) Multiome | 804 |
Genomic view of the USP39 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.