This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for VPS35. 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 = VPS35 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 VPS35, 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 |
|---|---|---|---|---|
| chr16:46,620,934–46,621,754 | 67.8 kb | Distal (>10kb) Multiome | 816 | |
| chr16:46,632,606–46,634,034 | 55.9 kb | Distal (>10kb) Multiome | 427 | |
| chr16:46,688,335–46,690,548 | 131 bp | At TSS Multiome | 1034 | |
| chr16:46,690,771–46,691,129 | 1.6 kb | Proximal (<10kb) | 246 | |
| chr16:46,739,861–46,740,427 | 51.0 kb | Distal (>10kb) Multiome | 134 | |
| chr16:46,789,580–46,790,544 | 100.9 kb | Distal (>10kb) Multiome | 725 | |
| chr16:46,830,588–46,832,033 | 142.2 kb | Distal (>10kb) Multiome | 792 | |
| chr16:46,883,418–46,885,208 | 195.0 kb | Distal (>10kb) Multiome | 969 | |
| chr16:46,885,524–46,886,746 | 197.2 kb | Distal (>10kb) Multiome | 318 | |
| chr16:46,972,819–46,974,091 | 284.5 kb | Distal (>10kb) Multiome | 975 |
Genomic view of the VPS35 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.