This gene encodes a member of a family of proteins containing one or more high mobility group DNA-binding motifs. The encoded protein plays an important role in maintaining stem cell populations, and may be aberrantly expressed in tumor cells. A mutation in this gene was associated with microphthalmia, syndromic 13. There are numerous pseudogenes of this gene on multiple chromosomes. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Transcription factors with Perturb-seq knockdown data for HMGB3. 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 = HMGB3 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 HMGB3, 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 |
|---|---|---|---|---|
| chrX:150,693,098–150,694,049 | 289.8 kb | Distal (>10kb) Multiome | 435 | |
| chrX:150,898,166–150,899,720 | 84.6 kb | Distal (>10kb) Multiome | 562 | |
| chrX:150,902,225–150,902,784 | 80.8 kb | Distal (>10kb) Multiome | 187 | |
| chrX:150,982,738–150,984,074 | 129 bp | At TSS Multiome | 454 | |
| chrX:150,990,944–150,991,277 | 7.6 kb | Proximal (<10kb) | 62 | |
| chrX:151,082,143–151,082,818 | 99.1 kb | Distal (>10kb) Multiome | 346 | |
| chrX:151,175,898–151,178,232 | 193.1 kb | Distal (>10kb) Multiome | 212 |
Genomic view of the HMGB3 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.