Predicted to be located in membrane. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for LINC00390. 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 = LINC00390 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 LINC00390, 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 |
|---|---|---|---|---|
| chr13:44,105,002–44,105,286 | 3.4 kb | Proximal (<10kb) | 22 | |
| chr13:44,108,414–44,108,986 | at TSS | At TSS | 389 | |
| chr13:44,117,050–44,117,238 | 8.4 kb | Proximal (<10kb) | 54 | |
| chr13:44,134,611–44,135,456 | 6.6 kb | Proximal (<10kb) | 6 | |
| chr13:44,140,091–44,140,583 | 1.4 kb | Proximal (<10kb) | 67 | |
| chr13:44,141,321–44,142,793 | at TSS | At TSS | 822 |
Genomic view of the LINC00390 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.