This gene belongs to a group of vacuolar protein sorting (VPS) genes that, when functionally impaired, disrupt the efficient delivery of vacuolar hydrolases. The protein encoded by this gene is a component of a large multimeric complex, termed the retromer complex, which is involved in retrograde transport of proteins from endosomes to the trans-Golgi network. This VPS protein may be involved in the formation of the inner shell of the retromer coat for retrograde vesicles leaving the prevacuolar compartment. Alternative splice variants encoding different isoforms and representing non-protein coding transcripts have been found for this gene. [provided by RefSeq, Aug 2013]
Transcription factors with Perturb-seq knockdown data for VPS29. 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 = VPS29 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 VPS29, 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 |
|---|---|---|---|---|
| chr12:110,223,831–110,224,526 | 278.1 kb | Distal (>10kb) Multiome | 199 | |
| chr12:110,280,425–110,282,158 | 220.9 kb | Distal (>10kb) Multiome | 888 | |
| chr12:110,403,190–110,403,822 | 98.4 kb | Distal (>10kb) Multiome | 779 | |
| chr12:110,431,453–110,431,925 | 70.5 kb | Distal (>10kb) Multiome | 461 | |
| chr12:110,449,732–110,450,544 | 51.8 kb | Distal (>10kb) Multiome | 883 | |
| chr12:110,468,018–110,469,597 | 32.8 kb | Distal (>10kb) Multiome | 1093 | |
| chr12:110,501,642–110,502,585 | 53 bp | At TSS Multiome | 1115 | |
| chr12:110,582,284–110,583,969 | 81.2 kb | Distal (>10kb) Multiome HiCAR | 740 | |
| chr12:110,613,705–110,614,482 | 111.9 kb | Distal (>10kb) Multiome | 791 | |
| chr12:110,688,496–110,690,180 | 187.2 kb | Distal (>10kb) Multiome | 414 | |
| chr12:110,742,238–110,743,370 | 240.9 kb | Distal (>10kb) Multiome | 801 | |
| chr12:110,772,664–110,773,461 | 270.9 kb | Distal (>10kb) Multiome | 88 | |
| chr12:110,846,588–110,847,239 | 344.8 kb | Distal (>10kb) Multiome HiCAR | 371 |
Genomic view of the VPS29 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.