This gene encodes a member of the phospholipase D (PLD) family of enzymes that catalyze the hydrolysis of membrane phospholipids. The encoded protein is a single-pass type II membrane protein and contains two PLD phosphodiesterase domains. This protein influences processing of amyloid-beta precursor protein. Mutations in this gene are associated with Alzheimer disease risk. Alternatively spliced transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Apr 2014]
Transcription factors with Perturb-seq knockdown data for PLD3. 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 = PLD3 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 PLD3, 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 |
|---|---|---|---|---|
| chr19:40,055,898–40,056,369 | 292.6 kb | Distal (>10kb) Multiome | 746 | |
| chr19:40,090,491–40,091,099 | 257.9 kb | Distal (>10kb) Multiome | 831 | |
| chr19:40,190,883–40,192,408 | 156.8 kb | Distal (>10kb) Multiome | 764 | |
| chr19:40,217,060–40,217,642 | 131.4 kb | Distal (>10kb) Multiome | 366 | |
| chr19:40,284,527–40,285,917 | 63.3 kb | Distal (>10kb) Multiome | 913 | |
| chr19:40,347,917–40,348,964 | 159 bp | At TSS Multiome | 843 | |
| chr19:40,365,649–40,366,111 | 17.1 kb | Distal (>10kb) Multiome | 244 | |
| chr19:40,398,541–40,399,285 | 50.2 kb | Distal (>10kb) Multiome | 234 | |
| chr19:40,403,323–40,404,681 | 55.0 kb | Distal (>10kb) Multiome | 638 | |
| chr19:40,420,702–40,421,699 | 72.4 kb | Distal (>10kb) Multiome | 966 | |
| chr19:40,424,783–40,426,631 | 77.3 kb | Distal (>10kb) Multiome | 954 | |
| chr19:40,433,505–40,434,546 | 85.3 kb | Distal (>10kb) Multiome | 791 | |
| chr19:40,442,698–40,445,144 | 94.5 kb | Distal (>10kb) Multiome | 994 | |
| chr19:40,465,326–40,466,635 | 117.2 kb | Distal (>10kb) Multiome | 815 | |
| chr19:40,487,850–40,488,306 | 139.4 kb | Distal (>10kb) Multiome | 193 | |
| chr19:40,519,457–40,519,993 | 171.0 kb | Distal (>10kb) Multiome | 222 | |
| chr19:40,528,978–40,529,879 | 180.6 kb | Distal (>10kb) Multiome | 601 | |
| chr19:40,529,987–40,530,863 | 182.0 kb | Distal (>10kb) Multiome | 384 | |
| chr19:40,549,036–40,549,555 | 200.7 kb | Distal (>10kb) Multiome | 372 | |
| chr19:40,570,181–40,571,253 | 222.1 kb | Distal (>10kb) Multiome | 598 | |
| chr19:40,576,133–40,577,495 | 228.1 kb | Distal (>10kb) Multiome | 616 | |
| chr19:40,596,828–40,597,429 | 248.4 kb | Distal (>10kb) Multiome | 354 | |
| chr19:40,598,094–40,598,871 | 249.9 kb | Distal (>10kb) Multiome | 606 | |
| chr19:40,603,345–40,604,624 | 255.4 kb | Distal (>10kb) Multiome | 889 | |
| chr19:40,604,983–40,606,597 | 257.0 kb | Distal (>10kb) Multiome | 708 | |
| chr19:40,609,543–40,610,691 | 261.4 kb | Distal (>10kb) Multiome | 519 | |
| chr19:40,612,884–40,615,179 | 265.0 kb | Distal (>10kb) Multiome | 595 | |
| chr19:40,623,557–40,624,516 | 275.3 kb | Distal (>10kb) Multiome | 454 | |
| chr19:40,634,333–40,634,959 | 285.9 kb | Distal (>10kb) Multiome | 629 |
Genomic view of the PLD3 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.