Enables cell-cell adhesion mediator activity and neurexin family protein binding activity. Involved in L-ascorbic acid metabolic process and regulation of synapse assembly. Predicted to be located in several cellular components, including Golgi membrane; dendrite; and postsynaptic density. Predicted to be part of protein-containing complex. Predicted to be active in several cellular components, including GABA-ergic synapse; lipid droplet; and postsynaptic density membrane. [provided by Alliance of Genome Resources, Apr 2025]
Transcription factors with Perturb-seq knockdown data for CLSTN3. 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 = CLSTN3 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 CLSTN3, 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 |
|---|---|---|---|---|
| chr12:6,851,017–6,853,279 | 278.1 kb | Distal (>10kb) Multiome | 966 | |
| chr12:6,866,801–6,870,175 | 262.9 kb | Distal (>10kb) Multiome | 887 | |
| chr12:6,871,062–6,874,199 | 258.1 kb | Distal (>10kb) Multiome | 947 | |
| chr12:6,890,735–6,891,820 | 239.2 kb | Distal (>10kb) Multiome | 908 | |
| chr12:6,904,217–6,905,282 | 225.6 kb | Distal (>10kb) Multiome | 566 | |
| chr12:6,914,274–6,914,898 | 216.0 kb | Distal (>10kb) Multiome | 536 | |
| chr12:6,924,156–6,924,592 | 205.9 kb | Distal (>10kb) Multiome | 458 | |
| chr12:6,925,828–6,926,431 | 204.4 kb | Distal (>10kb) Multiome | 407 | |
| chr12:6,927,411–6,928,051 | 202.6 kb | Distal (>10kb) Multiome | 493 | |
| chr12:6,936,709–6,938,342 | 192.4 kb | Distal (>10kb) Multiome | 1008 | |
| chr12:6,942,356–6,945,492 | 186.2 kb | Distal (>10kb) Multiome | 1205 | |
| chr12:6,945,587–6,947,099 | 184.0 kb | Distal (>10kb) Multiome | 618 | |
| chr12:6,961,769–6,963,542 | 167.3 kb | Distal (>10kb) Multiome | 682 | |
| chr12:6,964,932–6,965,569 | 165.2 kb | Distal (>10kb) Multiome | 549 | |
| chr12:6,970,111–6,971,189 | 159.7 kb | Distal (>10kb) Multiome | 899 | |
| chr12:7,018,028–7,019,126 | 111.7 kb | Distal (>10kb) Multiome | 824 | |
| chr12:7,108,059–7,109,582 | 21.1 kb | Distal (>10kb) Multiome | 818 | |
| chr12:7,128,716–7,128,968 | 1.5 kb | Proximal (<10kb) | 174 | |
| chr12:7,129,788–7,131,412 | 145 bp | At TSS Multiome | 619 | |
| chr12:7,188,394–7,190,508 | 58.1 kb | Distal (>10kb) Multiome | 769 |
Genomic view of the CLSTN3 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.