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 is a member of the Sec1 domain family, and shows a high degree of sequence similarity to mouse, rat and yeast Vps45. The exact function of this gene is not known, but its high expression in peripheral blood mononuclear cells suggests a role in trafficking proteins, including inflammatory mediators. Multiple alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jul 2013]
Transcription factors with Perturb-seq knockdown data for VPS45. 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 = VPS45 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 VPS45, 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 |
|---|---|---|---|---|
| chr1:149,812,136–149,812,633 | 255.4 kb | Distal (>10kb) Multiome | 190 | |
| chr1:149,885,029–149,889,131 | 179.5 kb | Distal (>10kb) Multiome HiCAR | 1126 | |
| chr1:149,899,425–149,900,227 | 168.1 kb | Distal (>10kb) Multiome | 650 | |
| chr1:149,927,507–149,928,019 | 139.9 kb | Distal (>10kb) Multiome | 744 | |
| chr1:150,010,143–150,011,088 | 57.1 kb | Distal (>10kb) Multiome | 961 | |
| chr1:150,066,903–150,067,886 | 143 bp | At TSS Multiome | 986 | |
| chr1:150,149,493–150,150,439 | 82.3 kb | Distal (>10kb) Multiome | 448 | |
| chr1:150,162,838–150,163,636 | 95.5 kb | Distal (>10kb) Multiome | 550 | |
| chr1:150,213,532–150,214,095 | 145.9 kb | Distal (>10kb) Multiome | 441 | |
| chr1:150,234,435–150,235,519 | 166.9 kb | Distal (>10kb) Multiome | 725 | |
| chr1:150,235,635–150,236,696 | 168.4 kb | Distal (>10kb) Multiome | 905 | |
| chr1:150,255,443–150,256,199 | 187.9 kb | Distal (>10kb) Multiome | 441 | |
| chr1:150,256,563–150,257,324 | 189.3 kb | Distal (>10kb) Multiome | 223 | |
| chr1:150,257,589–150,258,594 | 190.4 kb | Distal (>10kb) Multiome | 233 | |
| chr1:150,259,728–150,260,778 | 192.3 kb | Distal (>10kb) Multiome | 362 | |
| chr1:150,268,574–150,269,453 | 201.3 kb | Distal (>10kb) Multiome | 785 | |
| chr1:150,281,629–150,283,038 | 214.6 kb | Distal (>10kb) Multiome | 503 | |
| chr1:150,293,680–150,294,144 | 226.1 kb | Distal (>10kb) Multiome | 755 | |
| chr1:150,313,761–150,314,506 | 246.3 kb | Distal (>10kb) Multiome | 108 | |
| chr1:150,321,137–150,321,825 | 253.7 kb | Distal (>10kb) Multiome | 806 | |
| chr1:150,363,368–150,364,980 | 296.2 kb | Distal (>10kb) Multiome | 971 |
Genomic view of the VPS45 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.