This gene encodes a member of a superfamily of divalent cation-dependent phosphodiesterases. The encoded protein associates with CD40, tumor necrosis factor (TNF) receptor-75 and TNF receptor associated factors (TRAFs), and inhibits nuclear factor-kappa-B activation. This protein has sequence and structural similarities with APE1 endonuclease, which is involved in both DNA repair and the activation of transcription factors. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for TDP2. 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 = TDP2 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 TDP2, 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 |
|---|---|---|---|---|
| chr6:24,399,950–24,401,131 | 266.4 kb | Distal (>10kb) Multiome | 381 | |
| chr6:24,402,665–24,403,713 | 263.9 kb | Distal (>10kb) Multiome | 945 | |
| chr6:24,494,447–24,495,849 | 171.8 kb | Distal (>10kb) Multiome | 946 | |
| chr6:24,630,916–24,631,933 | 35.5 kb | Distal (>10kb) Multiome | 80 | |
| chr6:24,645,624–24,646,552 | 20.8 kb | Distal (>10kb) Multiome | 641 | |
| chr6:24,659,056–24,659,261 | 7.6 kb | Proximal (<10kb) | 206 | |
| chr6:24,666,308–24,667,466 | 40 bp | At TSS Multiome | 1037 | |
| chr6:24,719,378–24,722,053 | 54.3 kb | Distal (>10kb) Multiome | 1238 | |
| chr6:24,774,256–24,775,895 | 108.3 kb | Distal (>10kb) Multiome | 1073 | |
| chr6:24,910,313–24,911,578 | 244.2 kb | Distal (>10kb) Multiome | 372 |
Genomic view of the TDP2 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.