This gene encodes a member of the sorting nexin family. Members of this family contain a phox (PX) domain, which is a phosphoinositide binding domain, and are involved in intracellular trafficking. This protein does not contain a coiled coil region, like most family members. This protein interacts with phosphatidylinositol-3-phosphate, and is involved in protein trafficking. A pseudogene of this gene is present on the sex chromosomes. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Jul 2014]
Transcription factors with Perturb-seq knockdown data for SNX3. 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 = SNX3 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 SNX3, 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 |
|---|---|---|---|---|
| chr6:108,074,193–108,075,197 | 186.5 kb | Distal (>10kb) Multiome | 935 | |
| chr6:108,117,713–108,118,288 | 143.2 kb | Distal (>10kb) Multiome | 242 | |
| chr6:108,133,646–108,134,560 | 127.2 kb | Distal (>10kb) Multiome | 560 | |
| chr6:108,164,692–108,165,502 | 96.2 kb | Distal (>10kb) Multiome | 111 | |
| chr6:108,260,173–108,261,671 | 59 bp | At TSS Multiome | 970 | |
| chr6:108,294,541–108,295,678 | 33.7 kb | Distal (>10kb) Multiome | 880 | |
| chr6:108,557,184–108,561,557 | 299.6 kb | Distal (>10kb) Multiome | 1119 |
Genomic view of the SNX3 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.