In vertebrates, the genes encoding the class of transcription factors called homeobox genes are found in clusters named A, B, C, and D on four separate chromosomes. Expression of these proteins is spatially and temporally regulated during embryonic development. This gene is part of the A cluster on chromosome 7 and encodes a DNA-binding transcription factor which may regulate gene expression, morphogenesis, and differentiation. This gene is highly similar to the abdominal-B (Abd-B) gene of Drosophila. A specific translocation event which causes a fusion between this gene and the NUP98 gene has been associated with myeloid leukemogenesis. Read-through transcription exists between this gene and the upstream homeobox A10 (HOXA10) gene.[provided by RefSeq, Mar 2011]
Transcription factors with Perturb-seq knockdown data for HOXA9. 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 = HOXA9 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 HOXA9, 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 |
|---|---|---|---|---|
| chr7:27,160,568–27,161,432 | 8.3 kb | Proximal (<10kb) | 613 | |
| chr7:27,164,163–27,164,913 | 4.8 kb | Proximal (<10kb) | 152 | |
| chr7:27,169,371–27,170,025 | at TSS | At TSS | 215 | |
| chr7:27,171,388–27,171,582 | 1.7 kb | Proximal (<10kb) | 154 | |
| chr7:27,173,233–27,174,630 | 3.5 kb | Proximal (<10kb) | 329 | |
| chr7:27,175,708–27,176,093 | 6.0 kb | Proximal (<10kb) | 88 | |
| chr7:27,179,593–27,180,372 | 9.9 kb | Proximal (<10kb) | 400 |
Genomic view of the HOXA9 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.