Major histocompatibility (MHC) class II molecules are transmembrane proteins that have a central role in development and control of the immune system. The protein encoded by this gene, along with regulatory factor X-associated ankyrin-containing protein and regulatory factor-5, forms a complex that binds to the X box motif of certain MHC class II gene promoters and activates their transcription. Once bound to the promoter, this complex associates with the non-DNA-binding factor MHC class II transactivator, which controls the cell type specificity and inducibility of MHC class II gene expression. Mutations in this gene have been linked to bare lymphocyte syndrome type II, complementation group D. Transcript variants utilizing different polyA signals have been found for this gene. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for RFXAP. 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 = RFXAP 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 RFXAP, 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 |
|---|---|---|---|---|
| chr13:36,431,409–36,432,761 | 387.1 kb | Distal (>10kb) Multiome HiCAR | 369 | |
| chr13:36,673,749–36,675,136 | 145.2 kb | Distal (>10kb) Multiome | 286 | |
| chr13:36,761,910–36,762,570 | 57.1 kb | Distal (>10kb) Multiome | 247 | |
| chr13:36,813,292–36,813,531 | 5.7 kb | Proximal (<10kb) | 30 | |
| chr13:36,815,147–36,815,418 | 3.8 kb | Proximal (<10kb) | 25 | |
| chr13:36,818,153–36,820,403 | 70 bp | At TSS Multiome | 690 | |
| chr13:36,919,257–36,920,884 | 100.9 kb | Distal (>10kb) Multiome | 481 | |
| chr13:36,998,372–37,001,433 | 180.1 kb | Distal (>10kb) Multiome | 1090 | |
| chr13:37,058,947–37,060,264 | 240.5 kb | Distal (>10kb) Multiome | 801 |
Genomic view of the RFXAP 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.