This gene encodes a member of the U2AF65 family of proteins. The encoded protein is found in the nucleus, where it co-localizes with core spliceosomal proteins. It has been shown to play a role in both steroid hormone receptor-mediated transcription and alternative splicing, and it is also a transcriptional coregulator of the viral oncoprotein v-Rel. Multiple transcript variants have been observed for this gene. A related pseudogene has been identified on chromosome X. [provided by RefSeq, Aug 2011]
Transcription factors with Perturb-seq knockdown data for RBM39. 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 = RBM39 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 RBM39, 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 |
|---|---|---|---|---|
| chr20:35,454,521–35,455,845 | 287.1 kb | Distal (>10kb) Multiome | 1059 | |
| chr20:35,539,672–35,540,321 | 202.3 kb | Distal (>10kb) Multiome | 311 | |
| chr20:35,541,280–35,542,685 | 200.2 kb | Distal (>10kb) Multiome | 849 | |
| chr20:35,600,739–35,601,999 | 140.7 kb | Distal (>10kb) Multiome | 575 | |
| chr20:35,604,921–35,605,589 | 136.9 kb | Distal (>10kb) Multiome | 27 | |
| chr20:35,615,559–35,617,919 | 124.4 kb | Distal (>10kb) Multiome | 1169 | |
| chr20:35,618,589–35,619,849 | 122.8 kb | Distal (>10kb) Multiome | 865 | |
| chr20:35,664,428–35,665,171 | 77.3 kb | Distal (>10kb) Multiome | 1018 | |
| chr20:35,698,724–35,699,893 | 42.9 kb | Distal (>10kb) Multiome | 1035 | |
| chr20:35,741,040–35,741,226 | 1.0 kb | Proximal (<10kb) | 91 | |
| chr20:35,741,564–35,742,903 | 150 bp | At TSS Multiome | 1145 | |
| chr20:35,769,101–35,769,560 | 27.0 kb | Distal (>10kb) Multiome | 415 | |
| chr20:35,771,622–35,772,463 | 29.8 kb | Distal (>10kb) Multiome | 998 | |
| chr20:35,953,663–35,955,230 | 212.3 kb | Distal (>10kb) Multiome | 1166 | |
| chr20:36,010,700–36,011,324 | 268.7 kb | Distal (>10kb) Multiome | 70 |
Genomic view of the RBM39 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.