This gene is located within the Smith-Magenis syndrome region on chromosome 17. It is highly similar to its mouse counterpart and is expressed at high levels mainly in neuronal tissues. The protein encoded by this gene includes a polymorphic polyglutamine tract in the N-terminal domain. Expression of the mouse counterpart in neurons is induced by retinoic acid. This gene is associated with both the severity of the phenotype and the response to medication in schizophrenic patients. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RAI1. 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 = RAI1 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 RAI1, 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 |
|---|---|---|---|---|
| chr17:17,476,268–17,477,427 | 204.5 kb | Distal (>10kb) Multiome | 720 | |
| chr17:17,494,918–17,497,329 | 184.9 kb | Distal (>10kb) Multiome | 704 | |
| chr17:17,591,221–17,592,219 | 89.7 kb | Distal (>10kb) Multiome | 945 | |
| chr17:17,680,744–17,682,037 | 177 bp | At TSS Multiome | 507 | |
| chr17:17,682,791–17,683,426 | 1.5 kb | Proximal (<10kb) Multiome | 510 | |
| chr17:17,693,050–17,694,108 | 11.9 kb | Distal (>10kb) Multiome | 549 | |
| chr17:17,694,284–17,695,355 | 13.3 kb | Distal (>10kb) Multiome | 703 | |
| chr17:17,700,114–17,700,885 | 19.1 kb | Distal (>10kb) Multiome | 327 | |
| chr17:17,724,458–17,725,494 | 43.6 kb | Distal (>10kb) Multiome | 283 | |
| chr17:17,751,962–17,752,874 | 70.9 kb | Distal (>10kb) Multiome | 640 | |
| chr17:17,780,889–17,783,985 | 99.7 kb | Distal (>10kb) Multiome | 655 | |
| chr17:17,792,432–17,793,087 | 111.4 kb | Distal (>10kb) Multiome | 135 | |
| chr17:17,809,458–17,811,066 | 128.6 kb | Distal (>10kb) Multiome | 371 | |
| chr17:17,811,471–17,812,921 | 131.0 kb | Distal (>10kb) Multiome | 664 | |
| chr17:17,823,156–17,824,542 | 142.3 kb | Distal (>10kb) Multiome | 743 | |
| chr17:17,835,765–17,838,695 | 154.9 kb | Distal (>10kb) Multiome | 1030 | |
| chr17:17,839,788–17,841,046 | 158.8 kb | Distal (>10kb) Multiome | 927 | |
| chr17:17,921,363–17,921,988 | 240.2 kb | Distal (>10kb) Multiome | 341 | |
| chr17:17,943,271–17,943,954 | 262.1 kb | Distal (>10kb) Multiome | 143 | |
| chr17:17,971,984–17,973,164 | 291.2 kb | Distal (>10kb) Multiome | 716 |
Genomic view of the RAI1 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.