This gene encodes a protein that contains laminin EGF motifs, a pentaxin domain, and many fibronectin type III motifs. The protein is found in the basement membrane, and may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIa and retinitis pigmentosa. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2008]
Transcription factors with Perturb-seq knockdown data for USH2A. 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 = USH2A 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 USH2A, 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 |
|---|---|---|---|---|
| chr1:216,246,531–216,247,343 | 176.5 kb | Distal (>10kb) Multiome | 153 | |
| chr1:216,599,992–216,601,697 | 177.8 kb | Distal (>10kb) Multiome | 616 | |
| chr1:216,605,851–216,606,620 | 182.8 kb | Distal (>10kb) Multiome | 152 | |
| chr1:216,722,952–216,724,156 | 300.1 kb | Distal (>10kb) Multiome | 254 | |
| chr1:218,163,871–218,166,014 | 1741.3 kb | Distal (>10kb) Multiome HiCAR | 548 |
Genomic view of the USH2A 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.