The protein encoded by this gene is a protease that deubiquitinates target proteins such as ADORA2A and TRIM21. The encoded protein shuttles between the nucleus and cytoplasm and is involved in maintaining operational fidelity in the endoplasmic reticulum. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]
Transcription factors with Perturb-seq knockdown data for USP4. 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 = USP4 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 USP4, 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 |
|---|---|---|---|---|
| chr3:49,093,005–49,094,956 | 246.4 kb | Distal (>10kb) Multiome | 944 | |
| chr3:49,104,279–49,105,309 | 235.9 kb | Distal (>10kb) Multiome | 712 | |
| chr3:49,120,575–49,121,282 | 219.8 kb | Distal (>10kb) Multiome | 765 | |
| chr3:49,132,603–49,133,965 | 207.0 kb | Distal (>10kb) Multiome | 652 | |
| chr3:49,166,057–49,166,586 | 174.4 kb | Distal (>10kb) Multiome | 622 | |
| chr3:49,170,896–49,171,950 | 169.3 kb | Distal (>10kb) Multiome | 781 | |
| chr3:49,276,912–49,277,398 | 63.6 kb | Distal (>10kb) Multiome | 291 | |
| chr3:49,339,607–49,340,853 | 525 bp | At TSS Multiome | 1044 | |
| chr3:49,357,868–49,359,083 | 17.7 kb | Distal (>10kb) Multiome | 908 | |
| chr3:49,411,409–49,412,844 | 71.5 kb | Distal (>10kb) Multiome | 899 | |
| chr3:49,422,179–49,422,905 | 81.8 kb | Distal (>10kb) Multiome | 453 | |
| chr3:49,428,857–49,429,869 | 88.8 kb | Distal (>10kb) Multiome | 712 | |
| chr3:49,461,484–49,462,134 | 121.0 kb | Distal (>10kb) Multiome | 207 | |
| chr3:49,468,926–49,470,930 | 129.5 kb | Distal (>10kb) Multiome | 919 | |
| chr3:49,539,369–49,540,584 | 199.3 kb | Distal (>10kb) Multiome | 628 | |
| chr3:49,553,618–49,555,244 | 213.8 kb | Distal (>10kb) Multiome | 710 |
Genomic view of the USP4 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.