DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is intronless. It encodes an RNA-dependent ATPase. The encoded protein is localized in the mitochondria and the nucleus, and can be transported between the mitochondria and the nucleus. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for DDX28. 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 = DDX28 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 DDX28, 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 |
|---|---|---|---|---|
| chr16:67,806,066–67,807,386 | 216.5 kb | Distal (>10kb) Multiome | 914 | |
| chr16:67,816,404–67,816,888 | 206.5 kb | Distal (>10kb) Multiome | 690 | |
| chr16:67,833,426–67,834,269 | 189.3 kb | Distal (>10kb) Multiome | 838 | |
| chr16:67,841,337–67,843,276 | 181.1 kb | Distal (>10kb) Multiome | 927 | |
| chr16:67,846,090–67,847,897 | 176.5 kb | Distal (>10kb) Multiome | 1025 | |
| chr16:67,872,739–67,873,665 | 150.2 kb | Distal (>10kb) Multiome | 982 | |
| chr16:67,884,566–67,885,097 | 138.4 kb | Distal (>10kb) Multiome | 264 | |
| chr16:67,892,898–67,893,885 | 130.0 kb | Distal (>10kb) Multiome | 867 | |
| chr16:67,915,108–67,915,887 | 107.8 kb | Distal (>10kb) Multiome | 92 | |
| chr16:67,935,189–67,936,596 | 87.4 kb | Distal (>10kb) Multiome | 980 | |
| chr16:67,963,746–67,964,209 | 59.3 kb | Distal (>10kb) Multiome | 161 | |
| chr16:67,968,087–67,969,341 | 54.6 kb | Distal (>10kb) Multiome | 861 | |
| chr16:67,993,130–67,993,736 | 29.8 kb | Distal (>10kb) Multiome | 790 | |
| chr16:68,019,222–68,020,043 | 3.8 kb | Proximal (<10kb) Multiome | 108 | |
| chr16:68,022,490–68,023,556 | 30 bp | At TSS Multiome | 958 | |
| chr16:68,084,205–68,086,133 | 62.0 kb | Distal (>10kb) Multiome | 1092 | |
| chr16:68,235,016–68,238,254 | 212.9 kb | Distal (>10kb) Multiome | 1055 | |
| chr16:68,239,582–68,240,355 | 216.8 kb | Distal (>10kb) Multiome | 223 | |
| chr16:68,244,730–68,245,757 | 222.0 kb | Distal (>10kb) Multiome | 803 | |
| chr16:68,264,033–68,265,087 | 241.2 kb | Distal (>10kb) Multiome | 876 | |
| chr16:68,310,451–68,311,505 | 287.8 kb | Distal (>10kb) Multiome | 1061 |
Genomic view of the DDX28 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.