The protein encoded by this gene is involved in the motility of cilia and flagella. The encoded protein is essential for the assembly of dynein regulatory and inner dynein arm complexes, which regulate ciliary beat. Defects in this gene are a cause of primary ciliary dyskinesia type 14 (CILD14). [provided by RefSeq, Jul 2011]
Transcription factors with Perturb-seq knockdown data for CCDC39. 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 = CCDC39 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 CCDC39, 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 |
|---|---|---|---|---|
| chr3:179,652,424–179,653,975 | 1026.4 kb | Distal (>10kb) Multiome HiCAR | 805 | |
| chr3:180,601,567–180,602,844 | 77.3 kb | Distal (>10kb) Multiome | 891 | |
| chr3:180,678,942–180,680,367 | 47 bp | At TSS Multiome | 682 | |
| chr3:180,684,886–180,685,265 | 5.4 kb | Proximal (<10kb) | 20 | |
| chr3:180,911,839–180,913,627 | 233.0 kb | Distal (>10kb) Multiome | 821 |
Genomic view of the CCDC39 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.