The protein encoded by this gene is an ortholog of the Drosophila melanogaster capicua gene, and is a member of the high mobility group (HMG)-box superfamily of transcriptional repressors. This protein contains a conserved HMG domain that is involved in DNA binding and nuclear localization, and a conserved C-terminus. Studies suggest that the N-terminal region of this protein interacts with Atxn1 (GeneID:6310), to form a transcription repressor complex, and in vitro studies suggest that polyglutamine-expansion of ATXN1 may alter the repressor activity of this complex. Mutations in this gene have been associated with olidogdendrogliomas (PMID:21817013). In addition, translocation events resulting in gene fusions of this gene with both DUX4 (GeneID:100288687) and FOXO4 (GeneID:4303) have been associated with round cell sarcomas. There are multiple pseudogenes of this gene found on chromosomes 1, 4, 6, 7, 16, 20, and the Y chromosome. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Feb 2015]
Transcription factors with Perturb-seq knockdown data for CIC. 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 = CIC 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 CIC, 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 |
|---|---|---|---|---|
| chr19:41,993,779–41,994,412 | 275.0 kb | Distal (>10kb) Multiome | 360 | |
| chr19:41,998,577–41,999,349 | 270.4 kb | Distal (>10kb) Multiome | 292 | |
| chr19:42,075,557–42,076,657 | 193.2 kb | Distal (>10kb) Multiome | 846 | |
| chr19:42,095,735–42,096,278 | 173.2 kb | Distal (>10kb) Multiome | 107 | |
| chr19:42,132,949–42,133,545 | 136.0 kb | Distal (>10kb) Multiome | 447 | |
| chr19:42,176,787–42,177,398 | 92.1 kb | Distal (>10kb) Multiome | 381 | |
| chr19:42,216,521–42,218,719 | 51.5 kb | Distal (>10kb) Multiome | 841 | |
| chr19:42,219,693–42,220,678 | 49.0 kb | Distal (>10kb) Multiome | 735 | |
| chr19:42,241,985–42,243,820 | 26.3 kb | Distal (>10kb) Multiome | 891 | |
| chr19:42,244,086–42,245,258 | 24.4 kb | Distal (>10kb) Multiome | 768 | |
| chr19:42,253,030–42,256,178 | 15.4 kb | Distal (>10kb) Multiome | 900 | |
| chr19:42,267,812–42,269,463 | 365 bp | At TSS Multiome | 887 | |
| chr19:42,279,620–42,280,909 | 10.8 kb | Distal (>10kb) Multiome | 818 | |
| chr19:42,283,173–42,285,280 | 14.8 kb | Distal (>10kb) Multiome | 739 | |
| chr19:42,301,842–42,303,114 | 33.4 kb | Distal (>10kb) Multiome | 858 | |
| chr19:42,313,206–42,313,892 | 44.3 kb | Distal (>10kb) Multiome | 515 | |
| chr19:42,323,530–42,326,402 | 56.3 kb | Distal (>10kb) Multiome | 833 | |
| chr19:42,386,878–42,387,621 | 118.1 kb | Distal (>10kb) Multiome | 602 | |
| chr19:42,396,430–42,397,663 | 127.8 kb | Distal (>10kb) Multiome | 585 | |
| chr19:42,401,221–42,402,278 | 132.5 kb | Distal (>10kb) Multiome | 475 | |
| chr19:42,422,934–42,424,367 | 154.5 kb | Distal (>10kb) Multiome | 439 |
Genomic view of the CIC 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.