This gene is one of several human genes similar to the C. elegans gene Fox-1. This gene encodes an RNA binding protein that is thought to be a key regulator of alternative exon splicing in the nervous system and other cell types. The protein binds to a conserved UGCAUG element found downstream of many alternatively spliced exons and promotes inclusion of the alternative exon in mature transcripts. The protein also interacts with the estrogen receptor 1 transcription factor and regulates estrogen receptor 1 transcriptional activity. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RBFOX2. 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 = RBFOX2 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 RBFOX2, 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 |
|---|---|---|---|---|
| chr22:35,539,918–35,540,941 | 488.4 kb | Distal (>10kb) Multiome | 411 | |
| chr22:35,627,232–35,627,966 | 401.3 kb | Distal (>10kb) Multiome | 482 | |
| chr22:35,836,344–35,836,620 | 3.7 kb | Proximal (<10kb) | 272 | |
| chr22:35,840,363–35,840,720 | 79 bp | At TSS | 355 | |
| chr22:36,027,992–36,029,495 | 154 bp | At TSS Multiome | 652 | |
| chr22:36,065,574–36,066,549 | 37.2 kb | Distal (>10kb) Multiome | 778 | |
| chr22:36,123,849–36,124,433 | 95.3 kb | Distal (>10kb) Multiome | 670 | |
| chr22:36,161,582–36,162,255 | 133.1 kb | Distal (>10kb) Multiome | 66 | |
| chr22:36,172,028–36,172,599 | 143.5 kb | Distal (>10kb) Multiome | 53 |
Genomic view of the RBFOX2 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.