This gene belongs to the family of reticulon encoding genes. Reticulons are associated with the endoplasmic reticulum, and are involved in neuroendocrine secretion or in membrane trafficking in neuroendocrine cells. The product of this gene is a potent neurite outgrowth inhibitor which may also help block the regeneration of the central nervous system in higher vertebrates. Alternatively spliced transcript variants derived both from differential splicing and differential promoter usage and encoding different isoforms have been identified. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RTN4. 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 = RTN4 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 RTN4, 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 |
|---|---|---|---|---|
| chr2:54,945,613–54,946,419 | 104.4 kb | Distal (>10kb) Multiome | 135 | |
| chr2:55,048,854–55,051,460 | 127 bp | At TSS Multiome | 1172 | |
| chr2:55,133,866–55,134,461 | 83.5 kb | Distal (>10kb) Multiome | 417 | |
| chr2:55,223,149–55,223,979 | 173.1 kb | Distal (>10kb) Multiome | 386 | |
| chr2:55,231,636–55,233,143 | 181.8 kb | Distal (>10kb) Multiome | 993 | |
| chr2:55,268,856–55,269,481 | 218.7 kb | Distal (>10kb) Multiome | 1083 | |
| chr2:55,279,327–55,280,579 | 229.3 kb | Distal (>10kb) Multiome | 219 | |
| chr2:55,281,727–55,282,873 | 231.7 kb | Distal (>10kb) Multiome | 943 |
Genomic view of the RTN4 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.