This gene encodes a member of a family of large proteins containing PHD (plant homeo domain)-type zinc fingers. The encoded protein may be associated in a nuclear complex that functions in histone H4 acetylation. Alternative splicing results in multiple transcript variants encoding the same protein. [provided by RefSeq, Aug 2013]
Transcription factors with Perturb-seq knockdown data for JADE3. 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 = JADE3 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 JADE3, 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 |
|---|---|---|---|---|
| chrX:46,758,820–46,759,807 | 153.0 kb | Distal (>10kb) Multiome | 494 | |
| chrX:46,777,921–46,778,647 | 134.0 kb | Distal (>10kb) Multiome | 97 | |
| chrX:46,836,621–46,837,502 | 75.4 kb | Distal (>10kb) Multiome | 606 | |
| chrX:46,903,672–46,904,257 | 8.3 kb | Proximal (<10kb) Multiome | 417 | |
| chrX:46,912,095–46,913,434 | 241 bp | At TSS Multiome | 558 | |
| chrX:47,129,095–47,129,667 | 217.1 kb | Distal (>10kb) Multiome | 538 | |
| chrX:47,144,621–47,145,590 | 232.8 kb | Distal (>10kb) Multiome | 649 | |
| chrX:47,190,608–47,191,059 | 278.5 kb | Distal (>10kb) Multiome | 536 | |
| chrX:47,191,642–47,192,226 | 279.8 kb | Distal (>10kb) Multiome | 138 | |
| chrX:47,193,067–47,193,943 | 281.5 kb | Distal (>10kb) Multiome | 651 |
Genomic view of the JADE3 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.