This gene encodes a member of a family of proteins that function in the nervous system as receptors and cell adhesion molecules. Extensive alternative splicing and the use of alternative promoters results in multiple transcript variants and protein isoforms for this gene, but the full-length nature of many of these variants has not been determined. Transcripts that initiate from an upstream promoter encode alpha isoforms, which contain epidermal growth factor-like (EGF-like) sequences and laminin G domains. Transcripts initiating from the downstream promoter encode beta isoforms, which lack EGF-like sequences. Genetic variation at this locus has been associated with a range of behavioral phenotypes, including alcohol dependence and autism spectrum disorder. [provided by RefSeq, Dec 2012]
Transcription factors with Perturb-seq knockdown data for NRXN3. 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 = NRXN3 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 NRXN3, 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 |
|---|---|---|---|---|
| chr14:77,965,921–77,966,514 | 204.1 kb | Distal (>10kb) Multiome | 258 | |
| chr14:77,980,545–77,981,614 | 189.3 kb | Distal (>10kb) Multiome | 329 | |
| chr14:78,029,563–78,030,313 | 140.5 kb | Distal (>10kb) Multiome | 227 | |
| chr14:78,164,255–78,164,561 | 5.8 kb | Proximal (<10kb) | 134 | |
| chr14:78,170,012–78,170,807 | 7 bp | At TSS Multiome | 141 | |
| chr14:78,315,886–78,316,626 | 145.9 kb | Distal (>10kb) Multiome | 121 | |
| chr14:78,319,943–78,320,801 | 150.0 kb | Distal (>10kb) Multiome | 160 | |
| chr14:78,359,786–78,360,558 | 189.8 kb | Distal (>10kb) Multiome | 39 | |
| chr14:78,985,556–78,986,174 | 815.5 kb | Distal (>10kb) Multiome | 171 | |
| chr14:79,091,225–79,091,881 | 921.2 kb | Distal (>10kb) Multiome | 174 | |
| chr14:79,278,063–79,280,041 | 1108.9 kb | Distal (>10kb) Multiome | 466 | |
| chr14:79,280,183–79,280,585 | 771 bp | At TSS | 43 | |
| chr14:79,281,306–79,282,562 | 1.9 kb | Proximal (<10kb) | 92 | |
| chr14:79,306,553–79,307,134 | 1136.4 kb | Distal (>10kb) Multiome | 80 | |
| chr14:79,332,824–79,333,601 | 1162.8 kb | Distal (>10kb) Multiome | 75 | |
| chr14:79,377,693–79,378,630 | 1207.8 kb | Distal (>10kb) Multiome | 108 | |
| chr14:79,487,469–79,488,320 | 1317.5 kb | Distal (>10kb) Multiome | 67 | |
| chr14:79,548,849–79,549,889 | 1378.7 kb | Distal (>10kb) Multiome HiCAR | 125 |
Genomic view of the NRXN3 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.