Predicted to be involved in embryonic pattern specification and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of cell population proliferation. Predicted to be active in nucleus. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for RIPPLY3. 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 = RIPPLY3 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 RIPPLY3, 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 |
|---|---|---|---|---|
| chr21:36,747,471–36,748,528 | 258.8 kb | Distal (>10kb) Multiome | 325 | |
| chr21:36,965,990–36,967,232 | 40.0 kb | Distal (>10kb) Multiome | 770 | |
| chr21:36,989,570–36,990,911 | 16.6 kb | Distal (>10kb) Multiome | 1026 | |
| chr21:37,006,026–37,007,215 | 101 bp | At TSS Multiome | 280 | |
| chr21:37,008,843–37,009,149 | 2.1 kb | Proximal (<10kb) | 49 | |
| chr21:37,009,856–37,010,215 | 3.2 kb | Proximal (<10kb) | 597 | |
| chr21:37,072,329–37,074,488 | 66.4 kb | Distal (>10kb) Multiome | 994 | |
| chr21:37,220,678–37,221,494 | 214.5 kb | Distal (>10kb) Multiome | 881 | |
| chr21:37,257,305–37,258,840 | 251.4 kb | Distal (>10kb) Multiome | 787 | |
| chr21:37,266,801–37,268,388 | 260.9 kb | Distal (>10kb) Multiome | 1079 |
Genomic view of the RIPPLY3 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.