This gene encodes a highly conserved nonhistone protein, which is a member of the heterochromatin protein family. The protein is enriched in the heterochromatin and associated with centromeres. The protein has a single N-terminal chromodomain which can bind to histone proteins via methylated lysine residues, and a C-terminal chromo shadow-domain (CSD) which is responsible for the homodimerization and interaction with a number of chromatin-associated nonhistone proteins. The encoded product is involved in the formation of functional kinetochore through interaction with essential kinetochore proteins. The gene has a pseudogene located on chromosome 3. Multiple alternatively spliced variants, encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CBX5. 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 = CBX5 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 CBX5, 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 |
|---|---|---|---|---|
| chr12:53,984,667–53,985,381 | 295.1 kb | Distal (>10kb) Multiome | 456 | |
| chr12:54,017,619–54,018,921 | 262.1 kb | Distal (>10kb) Multiome | 663 | |
| chr12:54,125,925–54,126,686 | 153.9 kb | Distal (>10kb) Multiome | 244 | |
| chr12:54,159,055–54,159,510 | 120.8 kb | Distal (>10kb) Multiome | 263 | |
| chr12:54,188,672–54,189,215 | 91.1 kb | Distal (>10kb) Multiome | 529 | |
| chr12:54,214,692–54,215,229 | 65.2 kb | Distal (>10kb) Multiome | 646 | |
| chr12:54,216,935–54,217,348 | 63.0 kb | Distal (>10kb) Multiome | 450 | |
| chr12:54,217,640–54,218,303 | 62.0 kb | Distal (>10kb) Multiome | 212 | |
| chr12:54,259,188–54,260,497 | 20.4 kb | Distal (>10kb) Multiome HiCAR | 573 | |
| chr12:54,279,361–54,281,440 | 486 bp | At TSS Multiome | 1100 | |
| chr12:54,288,499–54,288,982 | 8.4 kb | Proximal (<10kb) | 311 | |
| chr12:54,300,732–54,301,299 | 20.9 kb | Distal (>10kb) Multiome HiCAR | 545 | |
| chr12:54,324,486–54,325,464 | 44.9 kb | Distal (>10kb) Multiome HiCAR | 885 | |
| chr12:54,358,730–54,359,779 | 79.2 kb | Distal (>10kb) Multiome HiCAR | 857 | |
| chr12:54,370,156–54,370,782 | 90.4 kb | Distal (>10kb) Multiome | 399 | |
| chr12:54,378,747–54,380,140 | 99.1 kb | Distal (>10kb) Multiome | 649 | |
| chr12:54,390,265–54,391,699 | 111.2 kb | Distal (>10kb) Multiome | 393 | |
| chr12:54,419,123–54,419,837 | 139.3 kb | Distal (>10kb) Multiome | 441 | |
| chr12:54,431,650–54,432,865 | 152.0 kb | Distal (>10kb) Multiome | 498 | |
| chr12:54,452,678–54,453,187 | 172.7 kb | Distal (>10kb) Multiome | 54 | |
| chr12:54,549,254–54,550,339 | 269.5 kb | Distal (>10kb) Multiome | 365 | |
| chr12:54,579,588–54,580,234 | 299.8 kb | Distal (>10kb) Multiome | 271 |
Genomic view of the CBX5 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.