Involved in endocytic recycling and retrograde transport, endosome to Golgi. Acts upstream of or within lysosomal transport. Located in several cellular components, including Golgi apparatus; perinuclear region of cytoplasm; and recycling endosome. Part of EARP complex and GARP complex. Implicated in pontocerebellar hypoplasia type 2E. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for VPS53. 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 = VPS53 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 VPS53, 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 |
|---|---|---|---|---|
| chr17:409,399–411,454 | 304.6 kb | Distal (>10kb) Multiome HiCAR | 665 | |
| chr17:714,554–715,298 | 42 bp | At TSS Multiome | 798 | |
| chr17:731,870–733,144 | 17.6 kb | Distal (>10kb) Multiome | 602 | |
| chr17:751,539–752,928 | 37.5 kb | Distal (>10kb) Multiome | 891 | |
| chr17:781,922–782,799 | 67.5 kb | Distal (>10kb) Multiome | 914 | |
| chr17:875,256–875,758 | 160.7 kb | Distal (>10kb) Multiome | 42 | |
| chr17:927,652–928,423 | 213.1 kb | Distal (>10kb) Multiome | 315 | |
| chr17:933,255–933,971 | 218.8 kb | Distal (>10kb) Multiome | 400 | |
| chr17:951,413–952,178 | 236.9 kb | Distal (>10kb) Multiome | 385 | |
| chr17:964,907–965,931 | 250.7 kb | Distal (>10kb) Multiome | 256 | |
| chr17:978,189–980,530 | 265.0 kb | Distal (>10kb) Multiome | 639 | |
| chr17:996,479–997,532 | 282.0 kb | Distal (>10kb) Multiome | 994 |
Genomic view of the VPS53 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.