This gene encodes a protein belonging to the vacuolar-protein-sorting-13 gene family. In yeast, vacuolar-protein-sorting-13 proteins are involved in trafficking of membrane proteins between the trans-Golgi network and the prevacuolar compartment. While several transcript variants may exist for this gene, the full-length natures of only two have been described to date. These two represent the major variants of this gene and encode distinct isoforms. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for VPS13D. 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 = VPS13D 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 VPS13D, 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 |
|---|---|---|---|---|
| chr1:11,934,261–11,935,008 | 295.4 kb | Distal (>10kb) Multiome | 809 | |
| chr1:11,979,601–11,980,894 | 249.7 kb | Distal (>10kb) Multiome | 932 | |
| chr1:12,019,010–12,020,110 | 210.6 kb | Distal (>10kb) Multiome | 841 | |
| chr1:12,049,082–12,050,305 | 180.1 kb | Distal (>10kb) Multiome | 142 | |
| chr1:12,067,600–12,068,080 | 162.2 kb | Distal (>10kb) Multiome | 128 | |
| chr1:12,078,792–12,079,863 | 150.4 kb | Distal (>10kb) Multiome | 281 | |
| chr1:12,166,812–12,167,546 | 63.0 kb | Distal (>10kb) Multiome | 414 | |
| chr1:12,208,729–12,209,345 | 21.0 kb | Distal (>10kb) Multiome | 331 | |
| chr1:12,229,625–12,230,345 | 51 bp | At TSS Multiome | 666 | |
| chr1:12,433,370–12,434,013 | 203.7 kb | Distal (>10kb) Multiome | 607 | |
| chr1:12,510,733–12,511,367 | 281.0 kb | Distal (>10kb) Multiome | 319 |
Genomic view of the VPS13D 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.