The product of this gene is a core component of the exon junction complex (EJC), a protein complex that is deposited on spliced mRNAs at exon-exon junctions and functions in nonsense-mediated mRNA decay (NMD). The encoded protein binds RNA and interacts with two other EJC core components. It is predominantly located in the cytoplasm, but shuttles into the nucleus where it localizes to nuclear speckles. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CASC3. 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 = CASC3 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 CASC3, 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 |
|---|---|---|---|---|
| chr17:39,926,716–39,928,343 | 212.6 kb | Distal (>10kb) Multiome | 942 | |
| chr17:39,952,356–39,953,923 | 187.2 kb | Distal (>10kb) Multiome | 598 | |
| chr17:39,979,964–39,981,234 | 159.7 kb | Distal (>10kb) Multiome | 1148 | |
| chr17:40,054,311–40,054,810 | 85.8 kb | Distal (>10kb) Multiome | 694 | |
| chr17:40,062,700–40,063,624 | 77.3 kb | Distal (>10kb) Multiome | 609 | |
| chr17:40,075,390–40,075,997 | 64.7 kb | Distal (>10kb) Multiome | 556 | |
| chr17:40,098,950–40,099,858 | 41.1 kb | Distal (>10kb) Multiome | 997 | |
| chr17:40,100,155–40,101,301 | 39.6 kb | Distal (>10kb) Multiome | 954 | |
| chr17:40,111,702–40,112,164 | 28.5 kb | Distal (>10kb) Multiome | 678 | |
| chr17:40,113,185–40,113,691 | 26.9 kb | Distal (>10kb) Multiome | 864 | |
| chr17:40,121,452–40,123,602 | 18.4 kb | Distal (>10kb) Multiome | 799 | |
| chr17:40,139,909–40,141,108 | 48 bp | At TSS Multiome | 1121 | |
| chr17:40,177,152–40,178,398 | 37.2 kb | Distal (>10kb) Multiome | 329 | |
| chr17:40,191,326–40,192,022 | 51.5 kb | Distal (>10kb) Multiome | 588 | |
| chr17:40,218,712–40,219,963 | 79.1 kb | Distal (>10kb) Multiome | 901 | |
| chr17:40,287,308–40,288,608 | 147.4 kb | Distal (>10kb) Multiome | 870 | |
| chr17:40,306,565–40,307,697 | 166.7 kb | Distal (>10kb) Multiome | 366 | |
| chr17:40,316,576–40,317,119 | 176.4 kb | Distal (>10kb) Multiome | 557 | |
| chr17:40,317,794–40,318,727 | 177.9 kb | Distal (>10kb) Multiome | 799 | |
| chr17:40,341,205–40,342,644 | 201.6 kb | Distal (>10kb) Multiome | 835 | |
| chr17:40,344,939–40,346,042 | 205.1 kb | Distal (>10kb) Multiome | 730 | |
| chr17:40,362,469–40,363,831 | 222.5 kb | Distal (>10kb) Multiome | 846 | |
| chr17:40,417,289–40,418,494 | 277.7 kb | Distal (>10kb) Multiome | 793 | |
| chr17:40,422,953–40,423,555 | 282.9 kb | Distal (>10kb) Multiome | 242 |
Genomic view of the CASC3 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.