This gene belongs to the homeobox family of genes. The homeobox genes encode a highly conserved family of transcription factors that play an important role in morphogenesis in all multicellular organisms. Mammals possess four similar homeobox gene clusters, HOXA, HOXB, HOXC and HOXD, located on different chromosomes, consisting of 9 to 11 genes arranged in tandem. This gene is one of several homeobox HOXD genes located in a cluster on chromosome 2. Deletions that remove the entire HOXD gene cluster or the 5' end of this cluster have been associated with severe limb and genital abnormalities. Mutations in this particular gene cause synpolydactyly. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for HOXD13. 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 = HOXD13 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 HOXD13, 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 |
|---|---|---|---|---|
| chr2:176,082,698–176,083,714 | 9.0 kb | Proximal (<10kb) | 171 | |
| chr2:176,085,189–176,085,595 | 7.1 kb | Proximal (<10kb) | 68 | |
| chr2:176,085,941–176,087,147 | 5.6 kb | Proximal (<10kb) | 275 | |
| chr2:176,087,237–176,089,163 | 3.6 kb | Proximal (<10kb) | 475 | |
| chr2:176,091,485–176,093,664 | at TSS | At TSS | 351 | |
| chr2:176,096,693–176,099,096 | 4.0 kb | Proximal (<10kb) | 661 | |
| chr2:176,099,289–176,100,524 | 6.6 kb | Proximal (<10kb) | 116 |
Genomic view of the HOXD13 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.