This gene encodes a spectrin repeat containing protein expressed in skeletal and smooth muscle, and peripheral blood lymphocytes, that localizes to the nuclear membrane. Mutations in this gene have been associated with autosomal recessive spinocerebellar ataxia 8, also referred to as autosomal recessive cerebellar ataxia type 1 or recessive ataxia of Beauce. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for SYNE1. 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 = SYNE1 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 SYNE1, 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 |
|---|---|---|---|---|
| chr6:151,493,661–151,494,985 | 808.0 kb | Distal (>10kb) Multiome HiCAR | 691 | |
| chr6:151,647,848–151,649,022 | 653.8 kb | Distal (>10kb) Multiome HiCAR | 205 | |
| chr6:151,683,003–151,684,338 | 618.5 kb | Distal (>10kb) Multiome HiCAR | 214 | |
| chr6:152,093,336–152,094,382 | 208.2 kb | Distal (>10kb) Multiome | 107 | |
| chr6:152,296,303–152,296,938 | 5.2 kb | Proximal (<10kb) | 80 | |
| chr6:152,297,066–152,297,532 | 4.6 kb | Proximal (<10kb) | 85 | |
| chr6:152,298,182–152,298,535 | 3.6 kb | Proximal (<10kb) | 24 | |
| chr6:152,299,450–152,299,635 | 2.5 kb | Proximal (<10kb) | 17 | |
| chr6:152,301,647–152,302,563 | 9 bp | At TSS Multiome | 910 | |
| chr6:152,313,686–152,314,958 | 12.2 kb | Distal (>10kb) Multiome | 299 |
Genomic view of the SYNE1 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.