Predicted to enable SNAP receptor activity. Predicted to be involved in several processes, including lysosomal transport; protein catabolic process; and retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum. Predicted to act upstream of or within endoplasmic reticulum tubular network organization and regulation of ER to Golgi vesicle-mediated transport. Located in endoplasmic reticulum. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for USE1. 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 = USE1 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 USE1, 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 |
|---|---|---|---|---|
| chr19:17,074,934–17,076,532 | 139.8 kb | Distal (>10kb) Multiome | 890 | |
| chr19:17,205,346–17,205,530 | 9.9 kb | Proximal (<10kb) | 217 | |
| chr19:17,209,430–17,210,427 | 5.6 kb | Proximal (<10kb) Multiome | 245 | |
| chr19:17,215,005–17,215,979 | 100 bp | At TSS Multiome | 897 | |
| chr19:17,225,705–17,226,889 | 11.0 kb | Distal (>10kb) Multiome | 870 | |
| chr19:17,234,748–17,236,650 | 20.5 kb | Distal (>10kb) Multiome | 612 | |
| chr19:17,244,882–17,247,104 | 30.7 kb | Distal (>10kb) Multiome | 862 | |
| chr19:17,247,935–17,248,860 | 33.2 kb | Distal (>10kb) Multiome | 588 | |
| chr19:17,266,931–17,267,755 | 51.9 kb | Distal (>10kb) Multiome | 720 | |
| chr19:17,281,537–17,283,120 | 67.4 kb | Distal (>10kb) Multiome | 669 | |
| chr19:17,292,242–17,293,049 | 77.3 kb | Distal (>10kb) Multiome | 513 | |
| chr19:17,302,721–17,303,771 | 88.1 kb | Distal (>10kb) Multiome | 636 | |
| chr19:17,305,286–17,306,514 | 90.3 kb | Distal (>10kb) Multiome | 947 | |
| chr19:17,309,159–17,310,151 | 94.1 kb | Distal (>10kb) Multiome | 741 | |
| chr19:17,327,532–17,329,548 | 112.6 kb | Distal (>10kb) Multiome | 370 | |
| chr19:17,334,287–17,335,052 | 119.4 kb | Distal (>10kb) Multiome | 870 | |
| chr19:17,336,574–17,338,240 | 122.1 kb | Distal (>10kb) Multiome | 924 | |
| chr19:17,340,311–17,341,226 | 125.3 kb | Distal (>10kb) Multiome | 419 | |
| chr19:17,390,414–17,391,521 | 175.8 kb | Distal (>10kb) Multiome | 615 | |
| chr19:17,394,998–17,395,433 | 179.9 kb | Distal (>10kb) Multiome | 403 | |
| chr19:17,398,863–17,399,537 | 183.8 kb | Distal (>10kb) Multiome | 132 | |
| chr19:17,403,087–17,404,355 | 188.1 kb | Distal (>10kb) Multiome | 211 | |
| chr19:17,419,503–17,420,821 | 204.5 kb | Distal (>10kb) Multiome | 869 | |
| chr19:17,424,865–17,425,411 | 209.7 kb | Distal (>10kb) Multiome | 328 | |
| chr19:17,448,174–17,448,841 | 233.3 kb | Distal (>10kb) Multiome | 392 | |
| chr19:17,468,858–17,470,905 | 254.7 kb | Distal (>10kb) Multiome | 743 | |
| chr19:17,488,739–17,489,689 | 273.8 kb | Distal (>10kb) Multiome | 381 | |
| chr19:17,511,113–17,512,592 | 296.1 kb | Distal (>10kb) Multiome | 1021 |
Genomic view of the USE1 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.