This gene encodes the mitochondrial form of a pyridoxal phosphate-dependent enzyme that catalyzes the reversible reaction of serine and tetrahydrofolate to glycine and 5,10-methylene tetrahydrofolate. The encoded product is primarily responsible for glycine synthesis. The activity of the encoded protein has been suggested to be the primary source of intracellular glycine. The gene which encodes the cytosolic form of this enzyme is located on chromosome 17. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Oct 2009]
Transcription factors with Perturb-seq knockdown data for SHMT2. 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 = SHMT2 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 SHMT2, 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 |
|---|---|---|---|---|
| chr12:57,006,056–57,006,942 | 223.2 kb | Distal (>10kb) Multiome | 422 | |
| chr12:57,078,210–57,079,177 | 150.8 kb | Distal (>10kb) Multiome | 778 | |
| chr12:57,086,367–57,089,469 | 140.8 kb | Distal (>10kb) Multiome | 1047 | |
| chr12:57,093,695–57,094,140 | 135.6 kb | Distal (>10kb) Multiome | 243 | |
| chr12:57,110,045–57,111,598 | 119.3 kb | Distal (>10kb) Multiome | 656 | |
| chr12:57,111,611–57,112,633 | 117.3 kb | Distal (>10kb) Multiome | 940 | |
| chr12:57,127,277–57,129,227 | 101.6 kb | Distal (>10kb) Multiome | 725 | |
| chr12:57,214,315–57,214,722 | 15.1 kb | Distal (>10kb) Multiome HiCAR | 318 | |
| chr12:57,215,826–57,217,972 | 13.0 kb | Distal (>10kb) Multiome HiCAR | 525 | |
| chr12:57,219,094–57,219,803 | 10.2 kb | Distal (>10kb) Multiome HiCAR | 71 | |
| chr12:57,224,526–57,225,152 | 4.7 kb | Proximal (<10kb) Multiome | 267 | |
| chr12:57,225,987–57,227,617 | 2.6 kb | Proximal (<10kb) Multiome | 236 | |
| chr12:57,229,358–57,230,407 | 90 bp | At TSS Multiome HiCAR | 739 | |
| chr12:57,234,986–57,235,550 | 5.3 kb | Proximal (<10kb) | 365 | |
| chr12:57,236,204–57,236,680 | 6.5 kb | Proximal (<10kb) | 133 | |
| chr12:57,237,027–57,237,584 | 7.3 kb | Proximal (<10kb) | 93 | |
| chr12:57,237,805–57,241,749 | 9.5 kb | Proximal (<10kb) Multiome HiCAR | 846 | |
| chr12:57,242,371–57,244,402 | 14.1 kb | Distal (>10kb) Multiome | 596 | |
| chr12:57,270,778–57,271,413 | 41.4 kb | Distal (>10kb) Multiome | 155 | |
| chr12:57,272,508–57,273,156 | 43.1 kb | Distal (>10kb) Multiome | 98 | |
| chr12:57,377,252–57,378,039 | 148.0 kb | Distal (>10kb) Multiome | 170 | |
| chr12:57,430,384–57,431,415 | 201.3 kb | Distal (>10kb) Multiome | 879 | |
| chr12:57,454,516–57,456,639 | 226.6 kb | Distal (>10kb) Multiome | 841 | |
| chr12:57,458,743–57,463,318 | 231.7 kb | Distal (>10kb) Multiome | 994 | |
| chr12:57,475,229–57,476,151 | 245.9 kb | Distal (>10kb) Multiome | 194 | |
| chr12:57,487,577–57,488,336 | 258.2 kb | Distal (>10kb) Multiome | 784 | |
| chr12:57,519,488–57,521,440 | 291.0 kb | Distal (>10kb) Multiome | 1029 | |
| chr12:57,521,541–57,523,658 | 293.0 kb | Distal (>10kb) Multiome | 960 | |
| chr12:57,604,466–57,605,404 | 375.1 kb | Distal (>10kb) Multiome HiCAR | 337 | |
| chr12:57,609,052–57,609,957 | 379.6 kb | Distal (>10kb) Multiome HiCAR | 83 |
Genomic view of the SHMT2 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.