This gene encodes a protein that is similar to the yeast suppressor of actin mutations 2 gene. The yeast protein forms a subunit of the tetrameric Golgi-associated retrograde protein complex that is involved in vesicle trafficking from from both early and late endosomes, back to the trans-Golgi network. This gene is located on chromosome 6 in a head-to-head orientation with the gene encoding ribosomal protein S18. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2014]
Transcription factors with Perturb-seq knockdown data for VPS52. 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 = VPS52 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 VPS52, 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 |
|---|---|---|---|---|
| chr6:32,971,467–32,973,408 | 299.8 kb | Distal (>10kb) Multiome | 1115 | |
| chr6:33,009,348–33,009,899 | 262.2 kb | Distal (>10kb) Multiome | 184 | |
| chr6:33,080,635–33,081,087 | 191.2 kb | Distal (>10kb) Multiome | 141 | |
| chr6:33,161,505–33,162,100 | 110.2 kb | Distal (>10kb) Multiome | 589 | |
| chr6:33,199,801–33,201,289 | 71.2 kb | Distal (>10kb) Multiome | 1049 | |
| chr6:33,204,263–33,205,422 | 67.3 kb | Distal (>10kb) Multiome | 762 | |
| chr6:33,208,069–33,208,990 | 63.3 kb | Distal (>10kb) Multiome | 858 | |
| chr6:33,248,132–33,249,983 | 23.6 kb | Distal (>10kb) Multiome | 961 | |
| chr6:33,271,370–33,272,508 | 73 bp | At TSS Multiome | 1058 | |
| chr6:33,276,685–33,277,905 | 5.6 kb | Proximal (<10kb) Multiome | 807 | |
| chr6:33,280,035–33,280,319 | 8.2 kb | Proximal (<10kb) | 342 | |
| chr6:33,288,941–33,289,881 | 17.5 kb | Distal (>10kb) Multiome | 701 | |
| chr6:33,297,445–33,300,232 | 26.0 kb | Distal (>10kb) Multiome | 1095 | |
| chr6:33,312,436–33,314,207 | 41.0 kb | Distal (>10kb) Multiome | 795 | |
| chr6:33,317,189–33,318,504 | 46.0 kb | Distal (>10kb) Multiome | 649 | |
| chr6:33,322,636–33,323,832 | 51.3 kb | Distal (>10kb) Multiome | 941 | |
| chr6:33,346,609–33,347,126 | 74.9 kb | Distal (>10kb) Multiome | 37 | |
| chr6:33,390,888–33,392,247 | 119.7 kb | Distal (>10kb) Multiome | 993 | |
| chr6:33,409,936–33,411,502 | 138.6 kb | Distal (>10kb) Multiome | 977 | |
| chr6:33,417,606–33,419,249 | 146.4 kb | Distal (>10kb) Multiome | 973 | |
| chr6:33,419,793–33,420,532 | 148.3 kb | Distal (>10kb) Multiome | 162 | |
| chr6:33,425,590–33,426,362 | 154.0 kb | Distal (>10kb) Multiome | 665 | |
| chr6:33,431,024–33,432,096 | 159.3 kb | Distal (>10kb) Multiome | 337 | |
| chr6:33,454,074–33,454,852 | 182.6 kb | Distal (>10kb) Multiome | 906 | |
| chr6:33,547,185–33,548,324 | 275.8 kb | Distal (>10kb) Multiome | 155 | |
| chr6:33,570,899–33,571,638 | 299.5 kb | Distal (>10kb) Multiome | 755 |
Genomic view of the VPS52 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.