This gene encodes a member of the DEAD box protein family. These proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) and 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 thought to play a role in the prognosis of patients with gastrointestinal stromal tumors. A pseudogene of this gene is present on chromosome 13. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013]
Transcription factors with Perturb-seq knockdown data for DDX39A. 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 = DDX39A 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 DDX39A, 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 |
|---|---|---|---|---|
| chr19:14,136,079–14,137,770 | 282.5 kb | Distal (>10kb) Multiome | 978 | |
| chr19:14,206,623–14,207,699 | 212.1 kb | Distal (>10kb) Multiome HiCAR | 444 | |
| chr19:14,247,378–14,248,008 | 171.7 kb | Distal (>10kb) Multiome | 109 | |
| chr19:14,248,166–14,249,635 | 170.6 kb | Distal (>10kb) Multiome | 230 | |
| chr19:14,264,813–14,266,130 | 153.9 kb | Distal (>10kb) Multiome | 223 | |
| chr19:14,294,831–14,295,420 | 124.2 kb | Distal (>10kb) Multiome | 60 | |
| chr19:14,363,590–14,364,020 | 55.6 kb | Distal (>10kb) Multiome | 402 | |
| chr19:14,405,442–14,406,893 | 13.2 kb | Distal (>10kb) Multiome | 662 | |
| chr19:14,418,847–14,419,795 | 86 bp | At TSS Multiome | 817 | |
| chr19:14,432,848–14,433,780 | 14.0 kb | Distal (>10kb) Multiome | 524 | |
| chr19:14,450,232–14,451,000 | 31.3 kb | Distal (>10kb) Multiome | 271 | |
| chr19:14,472,177–14,472,986 | 53.2 kb | Distal (>10kb) Multiome | 566 | |
| chr19:14,495,705–14,496,690 | 76.9 kb | Distal (>10kb) Multiome | 813 | |
| chr19:14,517,523–14,519,160 | 99.2 kb | Distal (>10kb) Multiome | 952 | |
| chr19:14,528,857–14,530,279 | 110.1 kb | Distal (>10kb) Multiome | 842 | |
| chr19:14,536,700–14,537,683 | 117.8 kb | Distal (>10kb) Multiome | 329 | |
| chr19:14,556,545–14,557,088 | 137.5 kb | Distal (>10kb) Multiome | 509 | |
| chr19:14,564,060–14,565,155 | 145.2 kb | Distal (>10kb) Multiome | 226 | |
| chr19:14,571,772–14,572,330 | 152.8 kb | Distal (>10kb) Multiome | 896 | |
| chr19:14,689,407–14,690,497 | 270.6 kb | Distal (>10kb) Multiome | 624 |
Genomic view of the DDX39A 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.