The WNT gene family consists of structurally related genes which encode secreted signaling proteins. These proteins have been implicated in oncogenesis and in several developmental processes, including regulation of cell fate and patterning during embryogenesis. This gene is a member of the WNT gene family. It encodes a protein which shows 98% amino acid identity to mouse Wnt3 protein, and 84% to human WNT3A protein, another WNT gene product. The mouse studies show the requirement of Wnt3 in primary axis formation in the mouse. Studies of the gene expression suggest that this gene may play a key role in some cases of human breast, rectal, lung, and gastric cancer through activation of the WNT-beta-catenin-TCF signaling pathway. This gene is clustered with WNT15, another family member, in the chromosome 17q21 region. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for WNT3. 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 = WNT3 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 WNT3, 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 |
|---|---|---|---|---|
| chr17:45,131,590–45,133,655 | 1638.9 kb | Distal (>10kb) Multiome HiCAR | 898 | |
| chr17:45,135,189–45,136,052 | 1636.7 kb | Distal (>10kb) Multiome HiCAR | 930 | |
| chr17:46,741,863–46,742,381 | 30.2 kb | Distal (>10kb) Multiome | 64 | |
| chr17:46,770,710–46,773,968 | 406 bp | At TSS Multiome | 1101 | |
| chr17:46,785,507–46,786,271 | 13.7 kb | Distal (>10kb) Multiome | 111 | |
| chr17:46,809,169–46,809,433 | 9.3 kb | Proximal (<10kb) | 168 | |
| chr17:46,814,387–46,815,027 | 3.7 kb | Proximal (<10kb) | 61 | |
| chr17:46,818,301–46,820,276 | 47.1 kb | Distal (>10kb) Multiome | 471 | |
| chr17:46,820,873–46,822,625 | 50.1 kb | Distal (>10kb) Multiome | 430 | |
| chr17:46,850,945–46,852,297 | 79.2 kb | Distal (>10kb) Multiome | 470 | |
| chr17:46,922,775–46,923,450 | 150.8 kb | Distal (>10kb) Multiome | 986 |
Genomic view of the WNT3 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.