Protein ubiquitination controls many intracellular processes, including cell cycle progression, transcriptional activation, and signal transduction. This dynamic process, involving ubiquitin conjugating enzymes and deubiquitinating enzymes, adds and removes ubiquitin. Deubiquitinating enzymes are cysteine proteases that specifically cleave ubiquitin from ubiquitin-conjugated protein substrates. This gene encodes a deubiquitinating enzyme which lies in a gene cluster on chromosome Xp11.23 [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for USP11. 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 = USP11 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 USP11, 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:47,129,095–47,129,667 | 103.7 kb | Distal (>10kb) Multiome | 538 | |
| chrX:47,144,621–47,145,590 | 87.9 kb | Distal (>10kb) Multiome | 649 | |
| chrX:47,190,608–47,191,059 | 42.3 kb | Distal (>10kb) Multiome | 536 | |
| chrX:47,191,642–47,192,226 | 41.0 kb | Distal (>10kb) Multiome | 138 | |
| chrX:47,193,067–47,193,943 | 39.3 kb | Distal (>10kb) Multiome | 651 | |
| chrX:47,217,449–47,219,337 | 15.0 kb | Distal (>10kb) Multiome | 736 | |
| chrX:47,232,860–47,233,865 | 553 bp | At TSS Multiome | 684 | |
| chrX:47,321,409–47,321,883 | 88.6 kb | Distal (>10kb) Multiome | 127 | |
| chrX:47,361,756–47,362,456 | 129.1 kb | Distal (>10kb) Multiome | 297 | |
| chrX:47,381,691–47,382,470 | 149.2 kb | Distal (>10kb) Multiome HiCAR | 17 | |
| chrX:47,482,474–47,483,311 | 249.8 kb | Distal (>10kb) Multiome | 573 | |
| chrX:47,523,425–47,523,870 | 290.6 kb | Distal (>10kb) Multiome HiCAR | 403 |
Genomic view of the USP11 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.