This gene belongs to the reticulon family of highly conserved genes that are preferentially expressed in neuroendocrine tissues. This family of proteins interact with, and modulate the activity of beta-amyloid converting enzyme 1 (BACE1), and the production of amyloid-beta. An increase in the expression of any reticulon protein substantially reduces the production of amyloid-beta, suggesting that reticulon proteins are negative modulators of BACE1 in cells. Alternatively spliced transcript variants encoding different isoforms have been found for this gene, and pseudogenes of this gene are located on chromosomes 4 and 12. [provided by RefSeq, May 2012]
Transcription factors with Perturb-seq knockdown data for RTN3. 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 = RTN3 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 RTN3, 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 |
|---|---|---|---|---|
| chr11:63,489,897–63,491,487 | 190.5 kb | Distal (>10kb) Multiome | 254 | |
| chr11:63,491,633–63,492,303 | 189.5 kb | Distal (>10kb) Multiome | 264 | |
| chr11:63,503,095–63,503,560 | 178.2 kb | Distal (>10kb) Multiome | 72 | |
| chr11:63,613,506–63,614,656 | 67.1 kb | Distal (>10kb) Multiome | 502 | |
| chr11:63,670,776–63,672,118 | 9.8 kb | Proximal (<10kb) Multiome | 715 | |
| chr11:63,680,920–63,682,270 | 18 bp | At TSS Multiome | 869 | |
| chr11:63,682,372–63,682,533 | 899 bp | At TSS | 177 | |
| chr11:63,761,764–63,765,204 | 82.7 kb | Distal (>10kb) Multiome | 463 | |
| chr11:63,767,471–63,769,982 | 86.1 kb | Distal (>10kb) Multiome | 627 | |
| chr11:63,813,022–63,814,238 | 132.0 kb | Distal (>10kb) Multiome | 704 | |
| chr11:63,838,214–63,839,799 | 157.5 kb | Distal (>10kb) Multiome | 687 | |
| chr11:63,888,171–63,888,861 | 207.1 kb | Distal (>10kb) Multiome | 565 | |
| chr11:63,909,610–63,910,221 | 228.5 kb | Distal (>10kb) Multiome | 113 | |
| chr11:63,916,069–63,921,372 | 238.0 kb | Distal (>10kb) Multiome | 929 | |
| chr11:63,938,087–63,939,846 | 257.3 kb | Distal (>10kb) Multiome | 852 | |
| chr11:63,974,156–63,975,123 | 293.1 kb | Distal (>10kb) Multiome | 918 |
Genomic view of the RTN3 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.