Enables RNA binding activity; RNA polymerase II complex binding activity; and identical protein binding activity. Involved in negative regulation of protein kinase activity; positive regulation of transcription by RNA polymerase II; and tRNA splicing, via endonucleolytic cleavage and ligation. Located in microtubule cytoskeleton; nucleoplasm; and perinuclear region of cytoplasm. Part of tRNA-splicing ligase complex. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for RTRAF. 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 = RTRAF 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 RTRAF, 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 |
|---|---|---|---|---|
| chr14:51,776,047–51,776,802 | 213.1 kb | Distal (>10kb) Multiome | 249 | |
| chr14:51,826,826–51,827,456 | 162.6 kb | Distal (>10kb) Multiome HiCAR | 39 | |
| chr14:51,827,934–51,828,961 | 161.1 kb | Distal (>10kb) Multiome HiCAR | 229 | |
| chr14:51,846,633–51,847,447 | 142.5 kb | Distal (>10kb) Multiome | 292 | |
| chr14:51,978,982–51,979,608 | 9.9 kb | Proximal (<10kb) | 274 | |
| chr14:51,988,342–51,988,728 | 816 bp | At TSS | 20 | |
| chr14:51,988,956–51,990,294 | 47 bp | At TSS Multiome | 755 | |
| chr14:52,067,674–52,070,026 | 79.7 kb | Distal (>10kb) Multiome | 507 | |
| chr14:52,267,300–52,269,041 | 278.2 kb | Distal (>10kb) Multiome | 262 |
Genomic view of the RTRAF 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.