This gene encodes the pro-alpha2 chain of type I collagen whose triple helix comprises two alpha1 chains and one alpha2 chain. Type I is a fibril-forming collagen found in most connective tissues and is abundant in bone, cornea, dermis and tendon. Mutations in this gene are associated with osteogenesis imperfecta types I-IV, Ehlers-Danlos syndrome type VIIB, recessive Ehlers-Danlos syndrome Classical type, idiopathic osteoporosis, and atypical Marfan syndrome. Symptoms associated with mutations in this gene, however, tend to be less severe than mutations in the gene for the alpha1 chain of type I collagen (COL1A1) reflecting the different role of alpha2 chains in matrix integrity. Three transcripts, resulting from the use of alternate polyadenylation signals, have been identified for this gene. [provided by R. Dalgleish, Feb 2008]
Transcription factors with Perturb-seq knockdown data for COL1A2. 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 = COL1A2 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 COL1A2, 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 |
|---|---|---|---|---|
| chr7:94,223,393–94,224,331 | 171.1 kb | Distal (>10kb) Multiome | 298 | |
| chr7:94,307,449–94,308,049 | 87.1 kb | Distal (>10kb) Multiome HiCAR | 51 | |
| chr7:94,338,572–94,339,474 | 55.9 kb | Distal (>10kb) Multiome | 144 | |
| chr7:94,374,301–94,375,925 | 19.5 kb | Distal (>10kb) Multiome | 250 | |
| chr7:94,392,127–94,392,356 | 2.5 kb | Proximal (<10kb) | 84 | |
| chr7:94,393,359–94,395,729 | 254 bp | At TSS Multiome | 479 | |
| chr7:94,404,436–94,404,637 | 9.5 kb | Proximal (<10kb) | 18 | |
| chr7:94,509,249–94,510,982 | 115.2 kb | Distal (>10kb) Multiome | 908 | |
| chr7:94,517,104–94,518,155 | 123.0 kb | Distal (>10kb) Multiome | 58 | |
| chr7:94,655,105–94,659,080 | 263.3 kb | Distal (>10kb) Multiome | 828 |
Genomic view of the COL1A2 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.