This gene encodes the alpha chain of one of the nonfibrillar collagens. The function of this gene product is not known, however, it has been detected at low levels in all connective tissue-producing cells so it may serve a general function in connective tissues. Unlike most of the collagens, which are secreted into the extracellular matrix, collagen XIII contains a transmembrane domain and the protein has been localized to the plasma membrane. The transcripts for this gene undergo complex and extensive splicing involving at least eight exons. Like other collagens, collagen XIII is a trimer; it is not known whether this trimer is composed of one or more than one alpha chain isomer. A number of alternatively spliced transcript variants have been described, but the full length nature of some of them has not been determined. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for COL13A1. 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 = COL13A1 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 COL13A1, 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 |
|---|---|---|---|---|
| chr10:69,568,733–69,569,392 | 232.9 kb | Distal (>10kb) Multiome | 99 | |
| chr10:69,573,228–69,573,810 | 228.4 kb | Distal (>10kb) Multiome | 284 | |
| chr10:69,629,756–69,630,921 | 171.7 kb | Distal (>10kb) Multiome | 567 | |
| chr10:69,800,189–69,800,398 | 1.5 kb | Proximal (<10kb) | 113 | |
| chr10:69,801,126–69,803,261 | 1.0 kb | Proximal (<10kb) Multiome | 527 | |
| chr10:69,876,839–69,877,624 | 75.3 kb | Distal (>10kb) Multiome | 45 | |
| chr10:70,052,471–70,054,619 | 250.8 kb | Distal (>10kb) Multiome | 577 | |
| chr10:70,075,065–70,075,566 | 273.3 kb | Distal (>10kb) Multiome | 23 |
Genomic view of the COL13A1 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.