This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
Transcription factors with Perturb-seq knockdown data for KDM5C. 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 = KDM5C 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 KDM5C, 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:52,934,457–52,935,577 | 290.2 kb | Distal (>10kb) Multiome | 844 | |
| chrX:52,995,188–52,996,036 | 229.6 kb | Distal (>10kb) Multiome | 504 | |
| chrX:53,048,205–53,048,827 | 176.7 kb | Distal (>10kb) Multiome | 184 | |
| chrX:53,081,783–53,082,862 | 143.0 kb | Distal (>10kb) Multiome | 557 | |
| chrX:53,088,446–53,088,904 | 136.5 kb | Distal (>10kb) Multiome | 204 | |
| chrX:53,093,602–53,094,629 | 131.2 kb | Distal (>10kb) Multiome | 585 | |
| chrX:53,224,805–53,225,756 | 153 bp | At TSS Multiome | 825 | |
| chrX:53,421,898–53,423,292 | 197.5 kb | Distal (>10kb) Multiome | 745 | |
| chrX:53,441,598–53,442,101 | 216.6 kb | Distal (>10kb) Multiome | 254 |
Genomic view of the KDM5C 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.