This gene encodes a leucine-rich cytoplasmic protein, which is highly similar to a mouse protein that negatively regulates Ca/calmodulin-dependent protein kinase II phosphorylation and may be essential for spatial learning processes. Several alternatively spliced transcript variants of this gene have been described. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for NCDN. 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 = NCDN 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 NCDN, 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 |
|---|---|---|---|---|
| chr1:35,268,326–35,269,324 | 289.0 kb | Distal (>10kb) Multiome | 761 | |
| chr1:35,390,839–35,391,860 | 166.6 kb | Distal (>10kb) Multiome | 219 | |
| chr1:35,554,954–35,555,177 | 2.7 kb | Proximal (<10kb) | 47 | |
| chr1:35,556,848–35,558,023 | 231 bp | At TSS Multiome | 894 | |
| chr1:35,573,081–35,573,635 | 15.6 kb | Distal (>10kb) Multiome | 174 | |
| chr1:35,577,045–35,577,930 | 19.8 kb | Distal (>10kb) Multiome | 235 | |
| chr1:35,641,114–35,641,872 | 83.8 kb | Distal (>10kb) Multiome | 824 | |
| chr1:35,707,208–35,708,693 | 150.1 kb | Distal (>10kb) Multiome | 388 | |
| chr1:35,717,979–35,719,281 | 161.1 kb | Distal (>10kb) Multiome | 558 | |
| chr1:35,769,208–35,770,406 | 212.2 kb | Distal (>10kb) Multiome | 929 | |
| chr1:35,807,537–35,808,824 | 250.2 kb | Distal (>10kb) Multiome | 575 |
Genomic view of the NCDN 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.