Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps16 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2009]
Transcription factors with Perturb-seq knockdown data for VPS16. 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 = VPS16 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 VPS16, 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 |
|---|---|---|---|---|
| chr20:2,651,802–2,653,286 | 188.2 kb | Distal (>10kb) Multiome | 1060 | |
| chr20:2,663,925–2,664,409 | 176.5 kb | Distal (>10kb) Multiome | 908 | |
| chr20:2,692,159–2,694,013 | 148.1 kb | Distal (>10kb) Multiome | 584 | |
| chr20:2,752,636–2,753,047 | 88.0 kb | Distal (>10kb) Multiome HiCAR | 395 | |
| chr20:2,800,326–2,801,021 | 40.0 kb | Distal (>10kb) Multiome | 349 | |
| chr20:2,840,006–2,841,330 | 91 bp | At TSS Multiome | 997 | |
| chr20:2,872,329–2,874,047 | 32.8 kb | Distal (>10kb) Multiome | 980 | |
| chr20:3,045,415–3,046,996 | 205.2 kb | Distal (>10kb) Multiome | 999 | |
| chr20:3,071,569–3,072,466 | 231.5 kb | Distal (>10kb) Multiome | 214 | |
| chr20:3,092,619–3,093,442 | 252.3 kb | Distal (>10kb) Multiome | 180 |
Genomic view of the VPS16 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.