This gene encodes a member of the F-box protein family which is characterized by an approximately 40 amino acid motif, the F-box. The F-box proteins constitute one of the four subunits of ubiquitin protein ligase complex called SCFs (SKP1-cullin-F-box), which function in phosphorylation-dependent ubiquitination. The F-box proteins are divided into 3 classes: Fbws containing WD-40 domains, Fbls containing leucine-rich repeats, and Fbxs containing either different protein-protein interaction modules or no recognizable motifs. The protein encoded by this gene belongs to the Fbls class and, in addition to an F-box, contains at least six highly degenerated leucine-rich repeats. This family member plays a role in epigenetic silencing. It nucleates at CpG islands and specifically demethylates both mono- and di-methylated lysine-36 of histone H3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2012]
Transcription factors with Perturb-seq knockdown data for KDM2A. 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 = KDM2A 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 KDM2A, 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 |
|---|---|---|---|---|
| chr11:66,842,896–66,843,952 | 275.9 kb | Distal (>10kb) Multiome | 843 | |
| chr11:66,855,758–66,857,980 | 262.9 kb | Distal (>10kb) Multiome | 795 | |
| chr11:66,882,995–66,883,462 | 236.0 kb | Distal (>10kb) Multiome | 277 | |
| chr11:66,957,708–66,959,038 | 160.7 kb | Distal (>10kb) Multiome | 957 | |
| chr11:67,023,002–67,023,688 | 95.8 kb | Distal (>10kb) Multiome | 243 | |
| chr11:67,056,596–67,057,312 | 62.4 kb | Distal (>10kb) Multiome | 382 | |
| chr11:67,071,470–67,071,999 | 47.5 kb | Distal (>10kb) Multiome HiCAR | 302 | |
| chr11:67,117,553–67,120,314 | 209 bp | At TSS Multiome | 762 | |
| chr11:67,239,493–67,240,241 | 120.7 kb | Distal (>10kb) Multiome | 792 | |
| chr11:67,265,898–67,267,077 | 147.2 kb | Distal (>10kb) Multiome | 471 | |
| chr11:67,288,260–67,289,971 | 169.9 kb | Distal (>10kb) Multiome | 985 | |
| chr11:67,302,488–67,304,170 | 184.2 kb | Distal (>10kb) Multiome | 661 | |
| chr11:67,316,992–67,318,501 | 198.5 kb | Distal (>10kb) Multiome | 918 | |
| chr11:67,352,967–67,354,228 | 234.4 kb | Distal (>10kb) Multiome | 781 | |
| chr11:67,372,171–67,373,596 | 253.8 kb | Distal (>10kb) Multiome | 497 | |
| chr11:67,391,276–67,392,428 | 272.6 kb | Distal (>10kb) Multiome | 957 | |
| chr11:67,401,038–67,402,351 | 282.6 kb | Distal (>10kb) Multiome | 741 | |
| chr11:67,420,418–67,421,666 | 302.0 kb | Distal (>10kb) Multiome | 648 | |
| chr11:67,428,036–67,428,950 | 309.2 kb | Distal (>10kb) Multiome | 813 | |
| chr11:67,443,182–67,444,063 | 324.4 kb | Distal (>10kb) Multiome | 612 | |
| chr11:67,464,410–67,465,252 | 345.5 kb | Distal (>10kb) Multiome | 710 | |
| chr11:67,468,551–67,469,666 | 350.0 kb | Distal (>10kb) Multiome | 774 | |
| chr11:67,482,830–67,483,745 | 363.9 kb | Distal (>10kb) Multiome | 969 | |
| chr11:67,504,073–67,506,408 | 387.1 kb | Distal (>10kb) Multiome | 769 | |
| chr11:67,507,504–67,509,030 | 389.1 kb | Distal (>10kb) Multiome | 897 |
Genomic view of the KDM2A 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.