Predicted to enable calcium-dependent phospholipid binding activity. Involved in positive regulation of dendrite extension. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for CPNE9. 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 = CPNE9 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 CPNE9, 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 |
|---|---|---|---|---|
| chr3:9,499,948–9,500,976 | 203.2 kb | Distal (>10kb) Multiome HiCAR | 320 | |
| chr3:9,552,048–9,552,879 | 151.4 kb | Distal (>10kb) Multiome | 372 | |
| chr3:9,553,391–9,554,161 | 149.9 kb | Distal (>10kb) Multiome | 128 | |
| chr3:9,649,068–9,649,746 | 54.5 kb | Distal (>10kb) Multiome | 793 | |
| chr3:9,703,572–9,705,701 | 1.3 kb | Proximal (<10kb) Multiome | 664 | |
| chr3:9,715,200–9,715,410 | at TSS | At TSS | 73 | |
| chr3:9,727,013–9,727,518 | 23.4 kb | Distal (>10kb) Multiome | 264 | |
| chr3:9,730,724–9,732,470 | 27.5 kb | Distal (>10kb) Multiome | 934 | |
| chr3:9,749,252–9,750,525 | 46.1 kb | Distal (>10kb) Multiome | 873 | |
| chr3:9,769,503–9,770,124 | 66.1 kb | Distal (>10kb) Multiome | 504 | |
| chr3:9,792,176–9,793,536 | 89.0 kb | Distal (>10kb) Multiome | 915 | |
| chr3:9,809,609–9,810,744 | 106.3 kb | Distal (>10kb) Multiome | 437 | |
| chr3:9,843,116–9,844,397 | 140.2 kb | Distal (>10kb) Multiome | 787 | |
| chr3:9,862,465–9,863,231 | 159.0 kb | Distal (>10kb) Multiome | 581 | |
| chr3:9,890,247–9,891,058 | 186.8 kb | Distal (>10kb) Multiome | 969 | |
| chr3:9,902,504–9,903,128 | 199.0 kb | Distal (>10kb) Multiome | 396 | |
| chr3:9,914,983–9,916,160 | 211.4 kb | Distal (>10kb) Multiome | 668 | |
| chr3:9,916,644–9,917,412 | 213.2 kb | Distal (>10kb) Multiome | 519 | |
| chr3:9,932,470–9,934,327 | 229.9 kb | Distal (>10kb) Multiome | 1035 | |
| chr3:9,946,152–9,947,739 | 243.6 kb | Distal (>10kb) Multiome | 898 | |
| chr3:9,951,898–9,952,503 | 248.4 kb | Distal (>10kb) Multiome | 484 | |
| chr3:9,986,547–9,987,409 | 283.1 kb | Distal (>10kb) Multiome | 907 | |
| chr3:10,008,678–10,009,458 | 305.3 kb | Distal (>10kb) Multiome | 240 | |
| chr3:10,010,580–10,011,700 | 307.4 kb | Distal (>10kb) Multiome | 540 |
Genomic view of the CPNE9 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.