The protein encoded by this gene is a negative regulator of autophagy and endocytic trafficking and controls endosome maturation. This protein contains two conserved domains, an N-terminal RUN domain and a C-terminal DUF4206 domain. The RUN domain is involved in Ras-like GTPase signaling, and the DUF4206 domain contains a diacylglycerol (DAG) binding-like motif. Mutation in this gene results in deletion of the DAG binding-like motif and causes a recessive ataxia. Alternatively spliced transcript variants encoding distinct isoforms have been found for this gene. [provided by RefSeq, Apr 2014]
Transcription factors with Perturb-seq knockdown data for RUBCN. 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 = RUBCN 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 RUBCN, 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 |
|---|---|---|---|---|
| chr3:197,464,855–197,465,525 | 271.8 kb | Distal (>10kb) Multiome | 302 | |
| chr3:197,509,884–197,510,593 | 226.6 kb | Distal (>10kb) Multiome | 656 | |
| chr3:197,527,591–197,529,092 | 208.5 kb | Distal (>10kb) Multiome | 184 | |
| chr3:197,540,773–197,541,383 | 195.8 kb | Distal (>10kb) Multiome | 172 | |
| chr3:197,541,675–197,542,327 | 194.9 kb | Distal (>10kb) Multiome | 188 | |
| chr3:197,547,230–197,547,930 | 189.3 kb | Distal (>10kb) Multiome | 223 | |
| chr3:197,554,469–197,556,297 | 180.7 kb | Distal (>10kb) Multiome | 577 | |
| chr3:197,573,028–197,573,650 | 163.6 kb | Distal (>10kb) Multiome | 442 | |
| chr3:197,736,285–197,737,626 | 100 bp | At TSS Multiome | 760 | |
| chr3:197,749,348–197,750,809 | 12.8 kb | Distal (>10kb) Multiome | 787 | |
| chr3:197,790,656–197,791,971 | 54.4 kb | Distal (>10kb) Multiome | 906 | |
| chr3:197,949,736–197,950,528 | 213.2 kb | Distal (>10kb) Multiome | 803 | |
| chr3:197,959,834–197,960,964 | 223.3 kb | Distal (>10kb) Multiome | 773 |
Genomic view of the RUBCN 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.