This gene represents a nuclear retinoic acid receptor. The encoded protein, retinoic acid receptor alpha, regulates transcription in a ligand-dependent manner. This gene has been implicated in regulation of development, differentiation, apoptosis, granulopoeisis, and transcription of clock genes. Translocations between this locus and several other loci have been associated with acute promyelocytic leukemia. Alternatively spliced transcript variants have been found for this locus.[provided by RefSeq, Sep 2010]
Transcription factors with Perturb-seq knockdown data for RARA. 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 = RARA 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 RARA, 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 |
|---|---|---|---|---|
| chr17:40,054,311–40,054,810 | 254.7 kb | Distal (>10kb) Multiome | 694 | |
| chr17:40,062,700–40,063,624 | 246.2 kb | Distal (>10kb) Multiome | 609 | |
| chr17:40,075,390–40,075,997 | 233.5 kb | Distal (>10kb) Multiome | 556 | |
| chr17:40,098,950–40,099,858 | 209.9 kb | Distal (>10kb) Multiome | 997 | |
| chr17:40,100,155–40,101,301 | 208.4 kb | Distal (>10kb) Multiome | 954 | |
| chr17:40,111,702–40,112,164 | 197.3 kb | Distal (>10kb) Multiome | 678 | |
| chr17:40,113,185–40,113,691 | 195.7 kb | Distal (>10kb) Multiome | 864 | |
| chr17:40,121,452–40,123,602 | 187.2 kb | Distal (>10kb) Multiome | 799 | |
| chr17:40,139,909–40,141,108 | 168.8 kb | Distal (>10kb) Multiome | 1121 | |
| chr17:40,177,152–40,178,398 | 131.7 kb | Distal (>10kb) Multiome | 329 | |
| chr17:40,191,326–40,192,022 | 117.4 kb | Distal (>10kb) Multiome | 588 | |
| chr17:40,218,712–40,219,963 | 89.8 kb | Distal (>10kb) Multiome | 901 | |
| chr17:40,287,308–40,288,608 | 21.4 kb | Distal (>10kb) Multiome | 870 | |
| chr17:40,306,565–40,307,697 | 1.5 kb | Proximal (<10kb) | 366 | |
| chr17:40,309,024–40,309,244 | at TSS | At TSS | 464 | |
| chr17:40,309,362–40,309,663 | 183 bp | At TSS | 334 | |
| chr17:40,316,576–40,317,119 | 7.6 kb | Proximal (<10kb) Multiome | 557 | |
| chr17:40,317,462–40,317,667 | 8.3 kb | Proximal (<10kb) | 212 | |
| chr17:40,317,794–40,318,727 | 9.0 kb | Proximal (<10kb) Multiome | 799 | |
| chr17:40,341,205–40,342,644 | 32.7 kb | Distal (>10kb) Multiome | 835 | |
| chr17:40,344,939–40,346,042 | 36.2 kb | Distal (>10kb) Multiome | 730 | |
| chr17:40,354,919–40,355,309 | 9.7 kb | Proximal (<10kb) | 516 | |
| chr17:40,362,469–40,363,831 | 53.7 kb | Distal (>10kb) Multiome | 846 | |
| chr17:40,417,289–40,418,494 | 108.9 kb | Distal (>10kb) Multiome | 793 | |
| chr17:40,422,953–40,423,555 | 114.0 kb | Distal (>10kb) Multiome | 242 | |
| chr17:40,442,866–40,444,146 | 134.3 kb | Distal (>10kb) Multiome | 774 | |
| chr17:40,499,140–40,499,767 | 190.4 kb | Distal (>10kb) Multiome | 358 |
Genomic view of the RARA 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.