Nuclear pore complexes (NPCs) regulate the transport of macromolecules between the nucleus and cytoplasm, and are composed of many polypeptide subunits, many of which belong to the nucleoporin family. This gene belongs to the nucleoporin gene family and encodes a 186 kDa precursor protein that undergoes autoproteolytic cleavage to generate a 98 kDa nucleoporin and 96 kDa nucleoporin. The 98 kDa nucleoporin contains a Gly-Leu-Phe-Gly (GLGF) repeat domain and participates in many cellular processes, including nuclear import, nuclear export, mitotic progression, and regulation of gene expression. The 96 kDa nucleoporin is a scaffold component of the NPC. Proteolytic cleavage is important for targeting of the proteins to the NPC. Translocations between this gene and many other partner genes have been observed in different leukemias. Rearrangements typically result in chimeras with the N-terminal GLGF domain of this gene to the C-terminus of the partner gene. Alternative splicing results in multiple transcript variants encoding different isoforms, at least two of which are proteolytically processed. Some variants lack the region that encodes the 96 kDa nucleoporin. [provided by RefSeq, Feb 2016]
Transcription factors with Perturb-seq knockdown data for NUP98. 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 = NUP98 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 NUP98, 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 |
|---|---|---|---|---|
| chr11:3,580,829–3,581,470 | 216.2 kb | Distal (>10kb) Multiome | 80 | |
| chr11:3,614,331–3,614,934 | 183.0 kb | Distal (>10kb) Multiome | 150 | |
| chr11:3,641,420–3,643,023 | 155.3 kb | Distal (>10kb) Multiome | 679 | |
| chr11:3,796,972–3,798,333 | 255 bp | At TSS Multiome | 985 | |
| chr11:3,807,708–3,808,953 | 10.8 kb | Distal (>10kb) Multiome | 598 | |
| chr11:3,824,581–3,825,191 | 27.4 kb | Distal (>10kb) Multiome | 332 | |
| chr11:3,840,339–3,841,901 | 43.6 kb | Distal (>10kb) Multiome | 853 | |
| chr11:3,854,400–3,856,473 | 57.7 kb | Distal (>10kb) Multiome | 929 | |
| chr11:4,094,080–4,095,334 | 297.2 kb | Distal (>10kb) Multiome | 925 |
Genomic view of the NUP98 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.