Enables DNA-binding transcription repressor activity, RNA polymerase II-specific; RNA polymerase II cis-regulatory region sequence-specific DNA binding activity; and chromatin binding activity. Involved in several processes, including negative regulation of autophagy; negative regulation of cellular senescence; and regulation of DNA-templated transcription. Located in cytoplasm and nucleoplasm. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for ZKSCAN3. 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 = ZKSCAN3 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 ZKSCAN3, 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 |
|---|---|---|---|---|
| chr6:28,079,998–28,081,441 | 269.8 kb | Distal (>10kb) Multiome | 1054 | |
| chr6:28,104,510–28,105,291 | 245.1 kb | Distal (>10kb) Multiome | 927 | |
| chr6:28,136,684–28,137,470 | 212.9 kb | Distal (>10kb) Multiome | 1035 | |
| chr6:28,141,479–28,142,195 | 208.1 kb | Distal (>10kb) Multiome | 1010 | |
| chr6:28,171,036–28,171,660 | 178.5 kb | Distal (>10kb) Multiome | 67 | |
| chr6:28,225,159–28,225,667 | 124.6 kb | Distal (>10kb) Multiome | 914 | |
| chr6:28,281,346–28,282,033 | 68.4 kb | Distal (>10kb) Multiome | 751 | |
| chr6:28,335,073–28,336,704 | 14.2 kb | Distal (>10kb) Multiome | 1036 | |
| chr6:28,349,817–28,350,289 | 88 bp | At TSS Multiome | 884 | |
| chr6:28,356,177–28,356,613 | 6.4 kb | Proximal (<10kb) Multiome | 569 | |
| chr6:28,357,204–28,357,431 | 7.3 kb | Proximal (<10kb) | 129 | |
| chr6:28,383,266–28,383,869 | 33.6 kb | Distal (>10kb) Multiome | 821 | |
| chr6:28,399,292–28,400,183 | 49.9 kb | Distal (>10kb) Multiome | 978 | |
| chr6:28,443,132–28,443,643 | 93.5 kb | Distal (>10kb) Multiome | 481 | |
| chr6:28,468,726–28,469,991 | 119.3 kb | Distal (>10kb) Multiome | 36 | |
| chr6:28,542,393–28,543,473 | 192.9 kb | Distal (>10kb) Multiome | 775 | |
| chr6:28,587,026–28,587,675 | 237.4 kb | Distal (>10kb) Multiome | 777 | |
| chr6:28,589,233–28,589,816 | 239.6 kb | Distal (>10kb) Multiome | 684 |
Genomic view of the ZKSCAN3 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.