This gene encodes a protein with a N-terminal SCAN domain, and the longer isoform contains nine C2H2-type zinc finger repeats in the C-terminal domain. The protein localizes to centromeres during interphase and early prophase, and different isoforms can repress or activate transcription in transfection studies. Multiple transcript variants encoding different isoforms have been found for this gene. Additional variants have been described, but their biological validity has not been determined. [provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for ZNF397. 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 = ZNF397 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 ZNF397, 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 |
|---|---|---|---|---|
| chr18:34,976,588–34,978,849 | 264.0 kb | Distal (>10kb) Multiome | 821 | |
| chr18:35,040,904–35,042,634 | 199.7 kb | Distal (>10kb) Multiome | 886 | |
| chr18:35,231,061–35,231,445 | 9.6 kb | Proximal (<10kb) | 317 | |
| chr18:35,240,066–35,241,553 | 66 bp | At TSS Multiome | 906 | |
| chr18:35,244,650–35,244,951 | 3.6 kb | Proximal (<10kb) | 9 | |
| chr18:35,289,760–35,290,683 | 49.2 kb | Distal (>10kb) Multiome | 970 | |
| chr18:35,343,705–35,344,835 | 103.3 kb | Distal (>10kb) Multiome | 916 | |
| chr18:35,376,423–35,377,702 | 136.2 kb | Distal (>10kb) Multiome | 673 | |
| chr18:35,488,095–35,488,748 | 247.5 kb | Distal (>10kb) Multiome | 82 | |
| chr18:35,496,979–35,498,336 | 256.7 kb | Distal (>10kb) Multiome | 1055 |
Genomic view of the ZNF397 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.