This locus may represent a gene involved in regulation of transcription elongation and chromatin remodeling, based on studies of similar proteins in other organisms. The encoded protein may bind single-stranded DNA. [provided by RefSeq, Sep 2010]
Transcription factors with Perturb-seq knockdown data for RTF1. 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 = RTF1 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 RTF1, 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 |
|---|---|---|---|---|
| chr15:41,230,581–41,231,535 | 186.1 kb | Distal (>10kb) Multiome | 1063 | |
| chr15:41,283,739–41,284,308 | 133.2 kb | Distal (>10kb) Multiome | 798 | |
| chr15:41,332,102–41,333,206 | 84.4 kb | Distal (>10kb) Multiome | 883 | |
| chr15:41,416,690–41,417,765 | 54 bp | At TSS Multiome | 734 | |
| chr15:41,493,120–41,493,918 | 76.5 kb | Distal (>10kb) Multiome | 692 | |
| chr15:41,543,905–41,544,403 | 127.1 kb | Distal (>10kb) Multiome | 687 | |
| chr15:41,558,746–41,559,337 | 142.0 kb | Distal (>10kb) Multiome | 358 | |
| chr15:41,621,149–41,622,233 | 204.7 kb | Distal (>10kb) Multiome | 998 | |
| chr15:41,636,747–41,637,351 | 219.9 kb | Distal (>10kb) Multiome | 46 | |
| chr15:41,659,914–41,660,957 | 243.3 kb | Distal (>10kb) Multiome | 850 |
Genomic view of the RTF1 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.