This gene encodes a protein that is necessary for motile cilia function. It functions in correct left-right axis formation by regulating the assembly of the inner dynein arm and the dynein regulatory complexes, which control ciliary beat. Mutations in this gene cause ciliary dyskinesia type 15, a disorder due to defects in cilia motility. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Aug 2011]
Transcription factors with Perturb-seq knockdown data for CCDC40. 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 = CCDC40 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 CCDC40, 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 |
|---|---|---|---|---|
| chr17:79,741,617–79,742,395 | 294.6 kb | Distal (>10kb) Multiome | 631 | |
| chr17:79,777,458–79,779,299 | 258.7 kb | Distal (>10kb) Multiome | 754 | |
| chr17:79,789,372–79,790,442 | 246.9 kb | Distal (>10kb) Multiome | 464 | |
| chr17:79,796,576–79,798,566 | 239.4 kb | Distal (>10kb) Multiome | 897 | |
| chr17:79,800,514–79,801,509 | 235.8 kb | Distal (>10kb) Multiome | 650 | |
| chr17:79,810,019–79,810,463 | 226.4 kb | Distal (>10kb) Multiome | 392 | |
| chr17:79,813,160–79,813,861 | 223.1 kb | Distal (>10kb) Multiome | 350 | |
| chr17:79,834,107–79,837,863 | 200.4 kb | Distal (>10kb) Multiome | 885 | |
| chr17:79,838,651–79,840,856 | 197.1 kb | Distal (>10kb) Multiome | 954 | |
| chr17:79,924,070–79,924,677 | 112.2 kb | Distal (>10kb) Multiome | 279 | |
| chr17:79,926,061–79,926,673 | 110.3 kb | Distal (>10kb) Multiome | 366 | |
| chr17:79,991,451–79,992,302 | 44.9 kb | Distal (>10kb) Multiome | 655 | |
| chr17:80,008,356–80,008,965 | 28.0 kb | Distal (>10kb) Multiome | 554 | |
| chr17:80,035,332–80,037,314 | 265 bp | At TSS Multiome | 852 | |
| chr17:80,101,092–80,102,236 | 64.8 kb | Distal (>10kb) Multiome | 851 | |
| chr17:80,146,527–80,148,008 | 110.6 kb | Distal (>10kb) Multiome | 955 | |
| chr17:80,219,620–80,221,064 | 183.8 kb | Distal (>10kb) Multiome | 809 | |
| chr17:80,260,016–80,260,559 | 223.7 kb | Distal (>10kb) Multiome | 677 | |
| chr17:80,260,789–80,261,746 | 224.9 kb | Distal (>10kb) Multiome | 896 | |
| chr17:80,308,064–80,309,516 | 271.7 kb | Distal (>10kb) Multiome | 193 |
Genomic view of the CCDC40 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.