The gene is a member of the inositol-polyphosphate 5-phosphatase family. The encoded protein interacts with the ras-related C3 botulinum toxin substrate 1, which causes translocation of the encoded protein to the plasma membrane where it inhibits clathrin-mediated endocytosis. Alternative splicing results in multiple transcript variants. [provided by RefSeq, May 2010]
Transcription factors with Perturb-seq knockdown data for SYNJ2. 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 = SYNJ2 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 SYNJ2, 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 |
|---|---|---|---|---|
| chr6:157,708,186–157,708,676 | 273.4 kb | Distal (>10kb) Multiome | 16 | |
| chr6:157,822,586–157,824,197 | 158.7 kb | Distal (>10kb) Multiome | 842 | |
| chr6:157,889,727–157,890,344 | 91.8 kb | Distal (>10kb) Multiome | 81 | |
| chr6:157,981,020–157,982,539 | 144 bp | At TSS Multiome | 932 | |
| chr6:157,985,682–157,986,063 | 3.8 kb | Proximal (<10kb) | 591 | |
| chr6:157,986,200–157,986,451 | 4.3 kb | Proximal (<10kb) | 535 | |
| chr6:158,167,710–158,168,897 | 186.4 kb | Distal (>10kb) Multiome | 961 | |
| chr6:158,231,543–158,233,134 | 250.3 kb | Distal (>10kb) Multiome | 898 |
Genomic view of the SYNJ2 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.