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. The protein encoded by this gene is a member of the DEAD box protein family and interacts with several spliceosomal proteins. In addition, the encoded protein may recognize the bacterial second messengers cyclic di-GMP and cyclic di-AMP, resulting in the induction of genes involved in the innate immune response. [provided by RefSeq, Jan 2017]
Transcription factors with Perturb-seq knockdown data for DDX41. 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 = DDX41 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 DDX41, 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 |
|---|---|---|---|---|
| chr5:177,303,008–177,304,238 | 213.3 kb | Distal (>10kb) Multiome | 850 | |
| chr5:177,309,549–177,310,172 | 207.1 kb | Distal (>10kb) Multiome | 373 | |
| chr5:177,311,267–177,313,178 | 204.7 kb | Distal (>10kb) Multiome | 798 | |
| chr5:177,351,374–177,352,243 | 165.1 kb | Distal (>10kb) Multiome | 832 | |
| chr5:177,362,756–177,363,624 | 153.8 kb | Distal (>10kb) Multiome | 479 | |
| chr5:177,366,082–177,368,548 | 149.8 kb | Distal (>10kb) Multiome | 626 | |
| chr5:177,370,255–177,371,449 | 146.1 kb | Distal (>10kb) Multiome | 584 | |
| chr5:177,402,327–177,404,671 | 112.5 kb | Distal (>10kb) Multiome | 807 | |
| chr5:177,425,334–177,427,296 | 90.5 kb | Distal (>10kb) Multiome | 982 | |
| chr5:177,446,196–177,448,203 | 70.2 kb | Distal (>10kb) Multiome | 826 | |
| chr5:177,453,910–177,456,838 | 61.5 kb | Distal (>10kb) Multiome | 1057 | |
| chr5:177,457,280–177,458,365 | 59.1 kb | Distal (>10kb) Multiome | 321 | |
| chr5:177,472,252–177,474,487 | 44.2 kb | Distal (>10kb) Multiome | 546 | |
| chr5:177,491,301–177,491,987 | 25.3 kb | Distal (>10kb) Multiome | 522 | |
| chr5:177,494,661–177,498,477 | 21.3 kb | Distal (>10kb) Multiome | 915 | |
| chr5:177,500,863–177,501,460 | 15.8 kb | Distal (>10kb) Multiome HiCAR | 378 | |
| chr5:177,516,515–177,517,551 | 128 bp | At TSS Multiome | 958 | |
| chr5:177,553,719–177,554,931 | 37.6 kb | Distal (>10kb) Multiome | 671 | |
| chr5:177,591,993–177,592,765 | 75.3 kb | Distal (>10kb) Multiome | 724 | |
| chr5:177,599,409–177,600,500 | 83.1 kb | Distal (>10kb) Multiome | 871 | |
| chr5:177,607,310–177,608,120 | 90.7 kb | Distal (>10kb) Multiome | 392 |
Genomic view of the DDX41 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.