This gene is a member of the UBA domain family, whose members include proteins having connections to ubiquitin and the ubiquitination pathway. The ubiquitin associated domain is thought to be a non-covalent ubiquitin binding domain consisting of a compact three helix bundle. This particular protein originates from a gene locus in a refined region on chromosome 9 undergoing loss of heterozygosity in nasopharyngeal carcinoma (NPC). Taking into account its cytogenetic location, this UBA domain family member is being studies as a putative target for mutation in nasopharyngeal carcinomas. Multiple alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jan 2010]
Transcription factors with Perturb-seq knockdown data for UBAP1. 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 = UBAP1 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 UBAP1, 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 |
|---|---|---|---|---|
| chr9:34,048,315–34,049,845 | 129.9 kb | Distal (>10kb) Multiome | 1045 | |
| chr9:34,049,943–34,050,924 | 128.5 kb | Distal (>10kb) Multiome | 283 | |
| chr9:34,126,146–34,127,302 | 52.4 kb | Distal (>10kb) Multiome | 826 | |
| chr9:34,176,156–34,176,522 | 2.5 kb | Proximal (<10kb) | 39 | |
| chr9:34,178,460–34,179,845 | 50 bp | At TSS Multiome | 814 | |
| chr9:34,328,711–34,329,961 | 150.4 kb | Distal (>10kb) Multiome | 768 | |
| chr9:34,363,597–34,364,212 | 184.9 kb | Distal (>10kb) Multiome | 104 | |
| chr9:34,374,953–34,375,681 | 196.2 kb | Distal (>10kb) Multiome | 432 | |
| chr9:34,376,008–34,377,655 | 198.0 kb | Distal (>10kb) Multiome | 779 | |
| chr9:34,379,248–34,381,674 | 201.9 kb | Distal (>10kb) Multiome | 763 | |
| chr9:34,456,881–34,459,235 | 279.6 kb | Distal (>10kb) Multiome | 704 |
Genomic view of the UBAP1 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.