This nuclear gene encodes a mitochondrial protein which belongs to the FRATAXIN family. The protein functions in regulating mitochondrial iron transport and respiration. The expansion of intronic trinucleotide repeat GAA from 8-33 repeats to >90 repeats results in Friedreich ataxia. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2016]
Transcription factors with Perturb-seq knockdown data for FXN. 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 = FXN 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 FXN, 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 |
|---|---|---|---|---|
| chr9:68,704,523–68,706,504 | 330.5 kb | Distal (>10kb) Multiome HiCAR | 702 | |
| chr9:68,755,540–68,756,160 | 279.8 kb | Distal (>10kb) Multiome | 164 | |
| chr9:68,779,458–68,780,758 | 255.7 kb | Distal (>10kb) Multiome | 827 | |
| chr9:68,871,983–68,872,511 | 163.5 kb | Distal (>10kb) Multiome | 208 | |
| chr9:68,894,403–68,895,261 | 141.0 kb | Distal (>10kb) Multiome | 84 | |
| chr9:69,027,702–69,027,902 | 7.9 kb | Proximal (<10kb) | 113 | |
| chr9:69,035,618–69,036,298 | 146 bp | At TSS Multiome | 819 | |
| chr9:69,036,526–69,036,715 | 765 bp | At TSS | 202 | |
| chr9:69,044,264–69,045,109 | 8.5 kb | Proximal (<10kb) | 121 | |
| chr9:69,120,411–69,122,618 | 86.1 kb | Distal (>10kb) Multiome | 809 | |
| chr9:69,173,641–69,174,717 | 138.3 kb | Distal (>10kb) Multiome | 542 | |
| chr9:69,324,469–69,325,896 | 289.1 kb | Distal (>10kb) Multiome | 399 |
Genomic view of the FXN 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.