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. The encoded protein may be involved in the placement of hindbrain segments in the proper location along the anterior-posterior axis during development. Two transcript variants encoding two different isoforms have been found for this gene, with only one of the isoforms containing the homeodomain region. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for HOXA1. 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 = HOXA1 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 HOXA1, 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 |
|---|---|---|---|---|
| chr7:27,087,824–27,088,552 | 7.4 kb | Proximal (<10kb) | 142 | |
| chr7:27,091,885–27,092,537 | 3.5 kb | Proximal (<10kb) | 166 | |
| chr7:27,094,336–27,094,532 | 1.5 kb | Proximal (<10kb) | 29 | |
| chr7:27,095,780–27,096,930 | at TSS | At TSS | 507 | |
| chr7:27,098,275–27,098,615 | 2.3 kb | Proximal (<10kb) | 146 | |
| chr7:27,102,914–27,103,245 | 6.9 kb | Proximal (<10kb) | 92 |
Genomic view of the HOXA1 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.