This gene encodes for a protein that in yeast forms part of a trimeric vacuolar-protein-sorting complex that is required for retrograde transport of proteins from prevacuoles to the late Golgi compartment. As in yeast, mammalian Vps54 proteins contain a coiled-coil region and dileucine motifs. Alternative splicing results in multiple transcript variants encoding different isoforms [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for VPS54. 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 = VPS54 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 VPS54, 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 |
|---|---|---|---|---|
| chr2:63,746,437–63,747,016 | 272.7 kb | Distal (>10kb) Multiome | 145 | |
| chr2:63,840,151–63,842,662 | 177.7 kb | Distal (>10kb) Multiome | 1134 | |
| chr2:63,950,012–63,950,802 | 68.8 kb | Distal (>10kb) Multiome | 117 | |
| chr2:64,018,646–64,019,987 | 122 bp | At TSS Multiome | 831 | |
| chr2:64,023,857–64,024,027 | 4.4 kb | Proximal (<10kb) | 145 | |
| chr2:64,073,896–64,076,052 | 55.4 kb | Distal (>10kb) Multiome | 154 | |
| chr2:64,114,439–64,115,073 | 95.2 kb | Distal (>10kb) Multiome | 98 | |
| chr2:64,143,692–64,145,137 | 125.1 kb | Distal (>10kb) Multiome | 843 | |
| chr2:64,227,941–64,228,667 | 208.9 kb | Distal (>10kb) Multiome | 493 | |
| chr2:64,251,480–64,252,200 | 232.2 kb | Distal (>10kb) Multiome | 104 | |
| chr2:64,252,396–64,252,854 | 233.3 kb | Distal (>10kb) Multiome | 93 | |
| chr2:64,276,376–64,277,307 | 257.3 kb | Distal (>10kb) Multiome | 252 |
Genomic view of the VPS54 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.