This gene encodes a mitochondrial protein that interacts with reticulon 4, which is a potent inhibitor of regeneration following spinal cord injury. This interaction may be important for reticulon-induced inhibition of neurite growth. Mutations in this gene can cause optic atrophy 10, with or without ataxia, cognitive disability, and seizures. There is a pseudogene for this gene on chromosome 12. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Transcription factors with Perturb-seq knockdown data for RTN4IP1. 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 = RTN4IP1 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 RTN4IP1, 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 |
|---|---|---|---|---|
| chr6:106,360,205–106,361,449 | 268.9 kb | Distal (>10kb) Multiome | 616 | |
| chr6:106,422,406–106,423,164 | 206.6 kb | Distal (>10kb) Multiome | 102 | |
| chr6:106,511,736–106,513,208 | 117.0 kb | Distal (>10kb) Multiome | 661 | |
| chr6:106,629,212–106,630,045 | 65 bp | At TSS Multiome | 661 | |
| chr6:106,973,315–106,975,918 | 345.5 kb | Distal (>10kb) Multiome HiCAR | 630 |
Genomic view of the RTN4IP1 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.