This gene encodes a protein involved in nonsense-mediated mRNA decay (NMD) as part of the mRNA surveillance complex. The protein has kinase activity and is thought to function in NMD by phosphorylating the regulator of nonsense transcripts 1 protein. Alternatively spliced transcript variants have been described, but their full-length nature has yet to be determined. [provided by RefSeq, Mar 2013]
Transcription factors with Perturb-seq knockdown data for SMG1. 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 = SMG1 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 SMG1, 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 |
|---|---|---|---|---|
| chr16:18,789,852–18,790,674 | 136.0 kb | Distal (>10kb) Multiome | 1043 | |
| chr16:18,800,801–18,802,152 | 124.7 kb | Distal (>10kb) Multiome | 1139 | |
| chr16:18,925,547–18,927,198 | 130 bp | At TSS Multiome | 788 | |
| chr16:18,983,732–18,984,444 | 57.6 kb | Distal (>10kb) Multiome | 817 | |
| chr16:19,067,380–19,068,213 | 141.3 kb | Distal (>10kb) Multiome | 982 | |
| chr16:19,086,334–19,086,896 | 160.2 kb | Distal (>10kb) Multiome | 852 | |
| chr16:19,113,633–19,114,626 | 187.6 kb | Distal (>10kb) Multiome | 801 | |
| chr16:19,167,649–19,168,727 | 241.5 kb | Distal (>10kb) Multiome | 572 |
Genomic view of the SMG1 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.