Enables RNA binding activity. Involved in cellular hyperosmotic response; cellular response to tumor necrosis factor; and negative regulation of programmed cell death. Located in cytosol. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for YBX3. 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 = YBX3 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 YBX3, 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 |
|---|---|---|---|---|
| chr12:10,211,987–10,214,332 | 510.7 kb | Distal (>10kb) Multiome HiCAR | 873 | |
| chr12:10,557,141–10,558,180 | 165.8 kb | Distal (>10kb) Multiome | 180 | |
| chr12:10,613,109–10,614,787 | 109.7 kb | Distal (>10kb) Multiome | 875 | |
| chr12:10,673,596–10,674,631 | 49.1 kb | Distal (>10kb) Multiome | 554 | |
| chr12:10,716,786–10,717,252 | 6.1 kb | Proximal (<10kb) | 282 | |
| chr12:10,719,131–10,719,274 | 8.4 kb | Proximal (<10kb) | 13 | |
| chr12:10,721,993–10,723,742 | 19 bp | At TSS Multiome | 885 | |
| chr12:11,500,146–11,501,129 | 777.4 kb | Distal (>10kb) Multiome HiCAR | 874 |
Genomic view of the YBX3 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.