This gene encodes a member of the DEAD box family of RNA-dependent ATPases that mediate ATP hydrolysis during pre-mRNA splicing. The encoded protein is an essential splicing factor required for association of U2 small nuclear ribonucleoprotein with pre-mRNA, and it also plays an important role in mRNA export from the nucleus to the cytoplasm. This gene belongs to a cluster of genes localized in the vicinity of the genes encoding tumor necrosis factor alpha and tumor necrosis factor beta. These genes are all within the human major histocompatibility complex class III region. Mutations in this gene may be associated with rheumatoid arthritis. Alternative splicing results in multiple transcript variants. Related pseudogenes have been identified on both chromosomes 6 and 11. Read-through transcription also occurs between this gene and the upstream ATP6V1G2 (ATPase, H+ transporting, lysosomal 13kDa, V1 subunit G2) gene. [provided by RefSeq, Feb 2011]
Transcription factors with Perturb-seq knockdown data for DDX39B. 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 = DDX39B 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 DDX39B, 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 |
|---|---|---|---|---|
| chr6:31,307,823–31,308,922 | 233.8 kb | Distal (>10kb) Multiome | 248 | |
| chr6:31,366,884–31,367,398 | 174.9 kb | Distal (>10kb) Multiome | 433 | |
| chr6:31,399,631–31,400,231 | 142.2 kb | Distal (>10kb) Multiome | 678 | |
| chr6:31,403,046–31,404,269 | 138.4 kb | Distal (>10kb) Multiome | 796 | |
| chr6:31,441,682–31,442,105 | 100.2 kb | Distal (>10kb) Multiome | 316 | |
| chr6:31,462,703–31,463,323 | 79.0 kb | Distal (>10kb) Multiome | 352 | |
| chr6:31,497,638–31,498,615 | 44.0 kb | Distal (>10kb) Multiome | 613 | |
| chr6:31,541,205–31,542,816 | 66 bp | At TSS Multiome | 1073 | |
| chr6:31,546,485–31,547,136 | 4.7 kb | Proximal (<10kb) Multiome | 589 | |
| chr6:31,547,301–31,547,742 | 5.6 kb | Proximal (<10kb) Multiome | 762 | |
| chr6:31,580,713–31,581,330 | 39.0 kb | Distal (>10kb) Multiome HiCAR | 745 | |
| chr6:31,619,744–31,621,435 | 78.5 kb | Distal (>10kb) Multiome HiCAR | 1127 | |
| chr6:31,651,682–31,653,297 | 110.7 kb | Distal (>10kb) Multiome | 1113 | |
| chr6:31,660,325–31,660,941 | 118.8 kb | Distal (>10kb) Multiome | 892 | |
| chr6:31,664,725–31,666,373 | 122.9 kb | Distal (>10kb) Multiome | 1039 | |
| chr6:31,682,887–31,683,880 | 141.3 kb | Distal (>10kb) Multiome | 248 | |
| chr6:31,702,816–31,703,520 | 161.3 kb | Distal (>10kb) Multiome | 875 | |
| chr6:31,713,576–31,714,641 | 172.1 kb | Distal (>10kb) Multiome | 171 | |
| chr6:31,728,852–31,730,814 | 188.2 kb | Distal (>10kb) Multiome | 979 | |
| chr6:31,739,236–31,740,741 | 197.9 kb | Distal (>10kb) Multiome | 1043 | |
| chr6:31,766,045–31,766,778 | 224.4 kb | Distal (>10kb) Multiome | 351 | |
| chr6:31,795,097–31,796,366 | 253.9 kb | Distal (>10kb) Multiome | 979 | |
| chr6:31,806,162–31,807,183 | 264.9 kb | Distal (>10kb) Multiome | 947 | |
| chr6:31,814,125–31,815,936 | 272.6 kb | Distal (>10kb) Multiome | 822 | |
| chr6:31,818,020–31,818,663 | 276.4 kb | Distal (>10kb) Multiome | 280 | |
| chr6:31,821,306–31,822,544 | 280.0 kb | Distal (>10kb) Multiome | 714 | |
| chr6:31,826,770–31,828,135 | 285.5 kb | Distal (>10kb) Multiome | 1000 | |
| chr6:31,834,277–31,835,371 | 292.7 kb | Distal (>10kb) Multiome | 1085 |
Genomic view of the DDX39B 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.