This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing multiprotein complexes that function through modifying chromatin structure to keep genes silent. A chromosomal translocation (X;13) involving this gene is associated with X-linked cognitive disability. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2010]
Transcription factors with Perturb-seq knockdown data for ZMYM3. 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 = ZMYM3 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 ZMYM3, 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 |
|---|---|---|---|---|
| chrX:71,053,141–71,053,663 | 200.7 kb | Distal (>10kb) Multiome | 90 | |
| chrX:71,067,771–71,068,927 | 185.6 kb | Distal (>10kb) Multiome | 846 | |
| chrX:71,095,671–71,096,651 | 158.2 kb | Distal (>10kb) Multiome | 450 | |
| chrX:71,103,137–71,103,903 | 150.6 kb | Distal (>10kb) Multiome | 375 | |
| chrX:71,181,957–71,182,785 | 71.9 kb | Distal (>10kb) Multiome | 615 | |
| chrX:71,253,398–71,253,642 | 497 bp | At TSS | 150 | |
| chrX:71,253,749–71,255,053 | 86 bp | At TSS Multiome | 607 | |
| chrX:71,255,169–71,255,415 | 1.0 kb | Proximal (<10kb) | 278 | |
| chrX:71,283,100–71,284,134 | 29.4 kb | Distal (>10kb) Multiome | 633 | |
| chrX:71,365,705–71,366,636 | 112.0 kb | Distal (>10kb) Multiome | 578 | |
| chrX:71,532,799–71,533,342 | 278.8 kb | Distal (>10kb) Multiome | 845 |
Genomic view of the ZMYM3 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.