This gene encodes a homeo-domain containing protein from a class of homeobox transcription factors which are conserved in vertebrates. Genes of this family are involved in the regulation of body development and morphogenesis. The most conserved genes, called HOX genes are found in special gene clusters. This gene belongs to the VAX subfamily and lies in the vicinity of the EMX homeobox gene family. Another member of VAX family is located on chromosome 2. The encoded protein may play an important role in the development of anterior ventral forebrain and visual system. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for VAX1. 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 = VAX1 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 VAX1, 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 |
|---|---|---|---|---|
| chr10:117,131,179–117,131,789 | 6.5 kb | Proximal (<10kb) | 130 | |
| chr10:117,132,643–117,133,100 | 5.2 kb | Proximal (<10kb) | 49 | |
| chr10:117,134,080–117,135,217 | 3.1 kb | Proximal (<10kb) | 216 | |
| chr10:117,136,430–117,136,650 | 1.6 kb | Proximal (<10kb) | 37 | |
| chr10:117,136,768–117,138,029 | 271 bp | At TSS | 337 | |
| chr10:117,138,165–117,138,497 | at TSS | At TSS | 108 | |
| chr10:117,138,997–117,141,025 | 696 bp | At TSS | 182 |
Genomic view of the VAX1 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.