This gene encodes a regulatory subunit of the SMG1 complex, which plays a critical role in nonsense-mediated mRNA decay (NMD). Binding of the encoded protein to the SMG1 complex kinase scaffold protein results in the inhibition of its kinase activity. Mutations in this gene cause a multiple congenital anomaly syndrome in human patients, characterized by brain malformation, congenital heart disease and other features. [provided by RefSeq, Jul 2016]
Transcription factors with Perturb-seq knockdown data for SMG9. 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 = SMG9 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 SMG9, 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 |
|---|---|---|---|---|
| chr19:43,463,046–43,464,465 | 291.4 kb | Distal (>10kb) Multiome | 645 | |
| chr19:43,474,993–43,475,696 | 279.6 kb | Distal (>10kb) Multiome | 506 | |
| chr19:43,503,542–43,505,032 | 250.7 kb | Distal (>10kb) Multiome | 760 | |
| chr19:43,526,489–43,527,639 | 227.7 kb | Distal (>10kb) Multiome | 712 | |
| chr19:43,532,595–43,534,553 | 220.8 kb | Distal (>10kb) Multiome | 698 | |
| chr19:43,575,342–43,576,244 | 179.3 kb | Distal (>10kb) Multiome | 562 | |
| chr19:43,580,271–43,581,020 | 174.3 kb | Distal (>10kb) Multiome | 151 | |
| chr19:43,594,710–43,596,874 | 158.7 kb | Distal (>10kb) Multiome | 998 | |
| chr19:43,618,905–43,620,391 | 135.2 kb | Distal (>10kb) Multiome | 1071 | |
| chr19:43,639,490–43,640,467 | 115.1 kb | Distal (>10kb) Multiome | 545 | |
| chr19:43,667,574–43,669,430 | 86.3 kb | Distal (>10kb) Multiome | 787 | |
| chr19:43,671,889–43,672,687 | 82.7 kb | Distal (>10kb) Multiome | 162 | |
| chr19:43,673,253–43,674,111 | 81.1 kb | Distal (>10kb) Multiome | 55 | |
| chr19:43,745,383–43,745,561 | 9.4 kb | Proximal (<10kb) | 159 | |
| chr19:43,754,239–43,755,900 | 201 bp | At TSS Multiome | 899 | |
| chr19:43,773,845–43,774,908 | 19.6 kb | Distal (>10kb) Multiome | 645 | |
| chr19:43,798,557–43,799,046 | 43.9 kb | Distal (>10kb) Multiome | 403 | |
| chr19:43,827,133–43,827,702 | 72.4 kb | Distal (>10kb) Multiome | 593 | |
| chr19:43,901,409–43,901,966 | 146.8 kb | Distal (>10kb) Multiome | 528 | |
| chr19:43,934,900–43,935,680 | 180.3 kb | Distal (>10kb) Multiome | 775 | |
| chr19:43,950,951–43,951,533 | 196.2 kb | Distal (>10kb) Multiome | 758 | |
| chr19:43,983,881–43,984,809 | 229.2 kb | Distal (>10kb) Multiome | 634 | |
| chr19:44,002,334–44,003,562 | 248.0 kb | Distal (>10kb) Multiome | 726 | |
| chr19:44,025,169–44,025,638 | 270.4 kb | Distal (>10kb) Multiome | 531 | |
| chr19:44,051,566–44,052,404 | 297.0 kb | Distal (>10kb) Multiome | 706 |
Genomic view of the SMG9 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.