This gene encodes the cytosolic form of serine hydroxymethyltransferase, a pyridoxal phosphate-containing enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. This reaction provides one-carbon units for synthesis of methionine, thymidylate, and purines in the cytoplasm. This gene is located within the Smith-Magenis syndrome region on chromosome 17. A pseudogene of this gene is located on the short arm of chromosome 1. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2013]
Transcription factors with Perturb-seq knockdown data for SHMT1. 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 = SHMT1 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 SHMT1, 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 |
|---|---|---|---|---|
| chr17:18,153,365–18,154,352 | 209.6 kb | Distal (>10kb) Multiome | 244 | |
| chr17:18,157,790–18,158,725 | 205.3 kb | Distal (>10kb) Multiome | 292 | |
| chr17:18,182,585–18,185,065 | 180.0 kb | Distal (>10kb) Multiome | 1051 | |
| chr17:18,224,148–18,226,173 | 138.8 kb | Distal (>10kb) Multiome | 680 | |
| chr17:18,246,777–18,247,912 | 116.3 kb | Distal (>10kb) Multiome | 314 | |
| chr17:18,257,865–18,259,083 | 104.9 kb | Distal (>10kb) Multiome | 684 | |
| chr17:18,260,145–18,261,582 | 102.9 kb | Distal (>10kb) Multiome | 778 | |
| chr17:18,314,513–18,315,715 | 48.4 kb | Distal (>10kb) Multiome | 865 | |
| chr17:18,363,090–18,363,830 | 14 bp | At TSS Multiome | 760 |
Genomic view of the SHMT1 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.