This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Dec 2010]
Transcription factors with Perturb-seq knockdown data for CLIP3. 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 = CLIP3 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 CLIP3, 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 |
|---|---|---|---|---|
| chr19:35,740,083–35,741,430 | 292.0 kb | Distal (>10kb) Multiome | 829 | |
| chr19:35,744,481–35,746,086 | 287.6 kb | Distal (>10kb) Multiome | 679 | |
| chr19:35,748,170–35,749,017 | 284.4 kb | Distal (>10kb) Multiome | 749 | |
| chr19:35,757,432–35,758,657 | 274.8 kb | Distal (>10kb) Multiome | 851 | |
| chr19:35,767,601–35,768,256 | 264.9 kb | Distal (>10kb) Multiome | 276 | |
| chr19:35,775,066–35,776,063 | 257.4 kb | Distal (>10kb) Multiome | 474 | |
| chr19:35,784,357–35,785,306 | 248.1 kb | Distal (>10kb) Multiome | 183 | |
| chr19:35,860,621–35,861,651 | 171.6 kb | Distal (>10kb) Multiome | 299 | |
| chr19:35,868,369–35,868,860 | 164.4 kb | Distal (>10kb) Multiome | 320 | |
| chr19:35,869,343–35,870,482 | 162.9 kb | Distal (>10kb) Multiome | 492 | |
| chr19:35,899,240–35,900,760 | 133.2 kb | Distal (>10kb) Multiome | 751 | |
| chr19:35,931,342–35,932,167 | 101.2 kb | Distal (>10kb) Multiome | 835 | |
| chr19:35,936,083–35,936,704 | 96.5 kb | Distal (>10kb) Multiome | 417 | |
| chr19:35,986,945–35,987,622 | 45.6 kb | Distal (>10kb) Multiome | 363 | |
| chr19:35,994,796–35,995,940 | 37.7 kb | Distal (>10kb) Multiome | 897 | |
| chr19:36,008,519–36,009,006 | 24.1 kb | Distal (>10kb) Multiome | 427 | |
| chr19:36,013,972–36,014,810 | 18.5 kb | Distal (>10kb) Multiome | 623 | |
| chr19:36,032,424–36,033,187 | 8 bp | At TSS Multiome | 179 | |
| chr19:36,053,782–36,055,591 | 21.6 kb | Distal (>10kb) Multiome | 1026 | |
| chr19:36,113,981–36,116,196 | 82.4 kb | Distal (>10kb) Multiome | 1052 | |
| chr19:36,127,575–36,128,707 | 95.2 kb | Distal (>10kb) Multiome | 942 | |
| chr19:36,139,425–36,141,811 | 108.4 kb | Distal (>10kb) Multiome | 1037 | |
| chr19:36,160,493–36,161,405 | 128.0 kb | Distal (>10kb) Multiome | 94 | |
| chr19:36,214,162–36,215,543 | 182.0 kb | Distal (>10kb) Multiome | 1008 | |
| chr19:36,245,106–36,245,849 | 212.6 kb | Distal (>10kb) Multiome | 153 | |
| chr19:36,331,415–36,332,377 | 298.9 kb | Distal (>10kb) Multiome | 372 |
Genomic view of the CLIP3 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.