This gene encodes a nuclear factor that is involved in the maintenance of pluripotency in stem cells and essential for embryogenesis. The encoded protein has a scaffold-attachment factor A/B, acinus and PIAS (SAP) domain that binds DNA and is thought to modify chromatin. Mice with a homozygous knockout of the orthologous gene die during late embryonic development or within hours after birth. Knockout embryos are normal in size at embryonic day 18.5 but exhibit skeletal and lung tissue abnormalities. This gene, when mutated, is highly expressed in embryonal carcinomas, pluripotent germ cell tumors, and other cancers and is thought to play an important role in tumor progression. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2017]
Transcription factors with Perturb-seq knockdown data for DPPA4. 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 = DPPA4 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 DPPA4, 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 |
|---|---|---|---|---|
| chr3:109,315,991–109,316,929 | 21.0 kb | Distal (>10kb) Multiome | 194 | |
| chr3:109,323,906–109,326,095 | 12.3 kb | Distal (>10kb) Multiome | 218 | |
| chr3:109,334,254–109,335,769 | 1.8 kb | Proximal (<10kb) | 43 | |
| chr3:109,336,338–109,336,883 | 638 bp | At TSS | 68 | |
| chr3:109,337,006–109,338,173 | 135 bp | At TSS Multiome | 155 | |
| chr3:109,338,868–109,339,179 | 1.3 kb | Proximal (<10kb) | 5 | |
| chr3:109,339,680–109,340,427 | 2.2 kb | Proximal (<10kb) | 127 | |
| chr3:109,340,697–109,341,112 | 3.2 kb | Proximal (<10kb) | 4 |
Genomic view of the DPPA4 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.