This non-coding locus is located in the HOX gene cluster. Transcription of this locus is induced by retinoic acid, and transcripts likely function in regulation of myelopoiesis through transcriptional activation of several genes in the HOXA cluster, in addition to several beta-2 integrins. [provided by RefSeq, Jan 2013]
Transcription factors with Perturb-seq knockdown data for HOTAIRM1. 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 = HOTAIRM1 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 HOTAIRM1, 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 | 7.6 kb | Proximal (<10kb) | 142 | |
| chr7:27,091,885–27,092,537 | 3.6 kb | Proximal (<10kb) | 166 | |
| chr7:27,094,336–27,094,532 | 1.6 kb | Proximal (<10kb) | 29 | |
| chr7:27,095,780–27,096,930 | at TSS | At TSS | 507 | |
| chr7:27,098,275–27,098,615 | 2.2 kb | Proximal (<10kb) | 146 | |
| chr7:27,102,914–27,103,245 | 6.8 kb | Proximal (<10kb) | 92 |
Genomic view of the HOTAIRM1 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.