This gene encodes a protein that is involved in lysosomal function. Mutations in this, as well as other neuronal ceroid-lipofuscinosis (CLN) genes, cause neurodegenerative diseases commonly known as Batten disease or collectively known as neuronal ceroid lipofuscinoses (NCLs). Many alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CLN3. 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 = CLN3 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 CLN3, 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 |
|---|---|---|---|---|
| chr16:28,211,165–28,212,644 | 279.9 kb | Distal (>10kb) Multiome | 960 | |
| chr16:28,267,361–28,267,924 | 224.4 kb | Distal (>10kb) Multiome | 36 | |
| chr16:28,277,564–28,278,417 | 214.1 kb | Distal (>10kb) Multiome | 598 | |
| chr16:28,291,632–28,293,697 | 198.5 kb | Distal (>10kb) Multiome | 578 | |
| chr16:28,491,428–28,492,451 | 74 bp | At TSS Multiome | 879 | |
| chr16:28,553,780–28,554,756 | 62.2 kb | Distal (>10kb) Multiome | 995 |
Genomic view of the CLN3 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.