This gene encodes a brain-specific membrane associated collagen. A product of proteolytic processing of the encoded protein, CLAC (collagenous Alzheimer amyloid plaque component), binds to amyloid beta-peptides found in Alzheimer amyloid plaques but CLAC inhibits rather than facilitates amyloid fibril elongation (PMID: 16300410). A study of over-expression of this collagen in mice, however, found changes in pathology and behavior suggesting that the encoded protein may promote amyloid plaque formation (PMID: 19548013). Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Dec 2011]
Transcription factors with Perturb-seq knockdown data for COL25A1. 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 = COL25A1 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 COL25A1, 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 |
|---|---|---|---|---|
| chr4:108,762,434–108,763,473 | 539.8 kb | Distal (>10kb) Multiome HiCAR | 593 | |
| chr4:109,294,116–109,294,307 | 8.4 kb | Proximal (<10kb) | 72 | |
| chr4:109,298,383–109,298,642 | 4.1 kb | Proximal (<10kb) | 24 | |
| chr4:109,298,744–109,298,909 | 3.8 kb | Proximal (<10kb) | 91 | |
| chr4:109,301,583–109,303,714 | 161 bp | At TSS Multiome | 426 | |
| chr4:109,375,427–109,376,315 | 73.1 kb | Distal (>10kb) Multiome | 86 | |
| chr4:109,386,823–109,387,310 | 84.3 kb | Distal (>10kb) Multiome | 74 | |
| chr4:109,419,054–109,420,658 | 117.1 kb | Distal (>10kb) Multiome | 227 | |
| chr4:109,433,232–109,434,512 | 131.0 kb | Distal (>10kb) Multiome | 802 | |
| chr4:109,559,632–109,561,390 | 257.4 kb | Distal (>10kb) Multiome | 756 |
Genomic view of the COL25A1 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.