This gene encodes an enzyme located in the peroxisomal membrane which is essential to the synthesis of ether phospholipids. Mutations in this gene are associated with rhizomelic chondrodysplasia punctata. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2015]
Transcription factors with Perturb-seq knockdown data for GNPAT. 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 = GNPAT 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 GNPAT, 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 |
|---|---|---|---|---|
| chr1:230,978,084–230,979,476 | 262.3 kb | Distal (>10kb) Multiome | 931 | |
| chr1:231,037,684–231,038,550 | 203.1 kb | Distal (>10kb) Multiome | 274 | |
| chr1:231,039,156–231,041,267 | 200.9 kb | Distal (>10kb) Multiome | 661 | |
| chr1:231,065,566–231,066,080 | 175.4 kb | Distal (>10kb) Multiome | 199 | |
| chr1:231,161,989–231,163,833 | 78.7 kb | Distal (>10kb) Multiome | 768 | |
| chr1:231,211,148–231,211,998 | 29.7 kb | Distal (>10kb) Multiome | 631 | |
| chr1:231,233,923–231,234,376 | 6.8 kb | Proximal (<10kb) | 288 | |
| chr1:231,240,746–231,241,633 | 43 bp | At TSS Multiome | 834 | |
| chr1:231,337,024–231,338,750 | 96.8 kb | Distal (>10kb) Multiome | 881 | |
| chr1:231,420,882–231,422,905 | 181.2 kb | Distal (>10kb) Multiome | 956 | |
| chr1:231,528,042–231,528,983 | 287.3 kb | Distal (>10kb) Multiome | 873 |
Genomic view of the GNPAT 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.