COL9A3

collagen type IX alpha 3 chain | DJ885L7.4.1, EDM3, FLJ90759, IDD, MED

This gene encodes one of the three alpha chains of type IX collagen, the major collagen component of hyaline cartilage. Type IX collagen, a heterotrimeric molecule, is usually found in tissues containing type II collagen, a fibrillar collagen. Mutations in this gene are associated with multiple epiphyseal dysplasia type 3. [provided by RefSeq, Jan 2010]

Developmental clusters: GC7

Biological processes 13 terms

basement membrane (GO:0005604)collagen type IX trimer (GO:0005594)collagen type IX trimer (GO:0005594)collagen type IX trimer (GO:0005594)endoplasmic reticulum lumen (GO:0005788)endoplasmic reticulum lumen (GO:0005788)extracellular matrix (GO:0031012)extracellular matrix organization (GO:0030198)extracellular matrix structural constituent conferring tensile strength (GO:0030020)extracellular matrix structural constituent conferring tensile strength (GO:0030020)extracellular matrix structural constituent conferring tensile strength (GO:0030020)extracellular region (GO:0005576)protein homodimerization activity (GO:0042803)

Expression (TPM)

TFs regulating COL9A3 0 TFs

Transcription factors with Perturb-seq knockdown data for COL9A3. 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 = COL9A3 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

Rows:

Elements linked to COL9A3

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of COL9A3, 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.

Element	Dist. to TSS	Link type	TFs
chr20:62,641,913–62,643,114	173.9 kb	Distal (>10kb) Multiome	874
chr20:62,791,452–62,791,941	24.6 kb	Distal (>10kb) Multiome	645
chr20:62,793,003–62,795,717	21.9 kb	Distal (>10kb) Multiome	1051
chr20:62,796,248–62,797,075	19.7 kb	Distal (>10kb) Multiome	566
chr20:62,808,356–62,808,554	7.7 kb	Proximal (<10kb)	312
chr20:62,815,479–62,817,462	744 bp	At TSS Multiome	503
chr20:62,824,643–62,825,353	8.8 kb	Proximal (<10kb) Multiome	339
chr20:62,860,497–62,862,892	45.7 kb	Distal (>10kb) Multiome	996
chr20:62,900,083–62,900,558	84.2 kb	Distal (>10kb) Multiome	764
chr20:62,925,950–62,926,856	110.3 kb	Distal (>10kb) Multiome	874
chr20:62,928,980–62,929,573	113.1 kb	Distal (>10kb) Multiome	289
chr20:62,937,285–62,938,569	121.8 kb	Distal (>10kb) Multiome	1026
chr20:63,006,367–63,007,246	190.7 kb	Distal (>10kb) Multiome	189
chr20:63,071,594–63,072,696	255.7 kb	Distal (>10kb) Multiome	246

Genome Browser

Genomic view of the COL9A3 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.