This gene encodes a member of the LIM homeobox gene family of developmentally expressed transcription factors. The encoded protein contains a homeodomain and two cysteine-rich zinc-binding LIM domains involved in protein-protein interactions. The protein is highly similar to a mouse protein that causes gonadal agenesis when inactivated, suggesting a role in gonadal development. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for LHX9. 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 = LHX9 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 LHX9, 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 |
|---|---|---|---|---|
| chr1:197,902,087–197,903,468 | 8.4 kb | Proximal (<10kb) | 980 | |
| chr1:197,908,736–197,909,098 | 2.8 kb | Proximal (<10kb) | 95 | |
| chr1:197,910,581–197,914,043 | at TSS | At TSS | 366 | |
| chr1:197,914,596–197,914,941 | 2.7 kb | Proximal (<10kb) | 79 | |
| chr1:197,915,230–197,918,701 | 3.3 kb | Proximal (<10kb) | 575 | |
| chr1:197,919,685–197,920,782 | 7.8 kb | Proximal (<10kb) | 152 | |
| chr1:197,921,162–197,922,078 | 9.3 kb | Proximal (<10kb) | 153 | |
| chr1:197,922,997–197,923,371 | 7.2 kb | Proximal (<10kb) | 30 | |
| chr1:197,924,603–197,924,824 | 8.8 kb | Proximal (<10kb) | 123 |
Genomic view of the LHX9 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.