This gene encodes a member of the cingulin family. The encoded protein localizes to both adherens and tight cell-cell junctions and mediates junction assembly and maintenance by regulating the activity of the small GTPases RhoA and Rac1. Heterozygous chromosomal rearrangements resulting in association of the promoter for this gene with the aromatase gene are a cause of aromatase excess syndrome. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Nov 2011]
Transcription factors with Perturb-seq knockdown data for CGNL1. 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 = CGNL1 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 CGNL1, 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 |
|---|---|---|---|---|
| chr15:57,198,642–57,199,172 | 177.7 kb | Distal (>10kb) Multiome | 193 | |
| chr15:57,255,638–57,256,396 | 120.4 kb | Distal (>10kb) Multiome | 74 | |
| chr15:57,259,456–57,260,042 | 116.7 kb | Distal (>10kb) Multiome | 261 | |
| chr15:57,306,141–57,307,417 | 69.7 kb | Distal (>10kb) Multiome | 512 | |
| chr15:57,321,974–57,322,475 | 54.2 kb | Distal (>10kb) Multiome | 391 | |
| chr15:57,323,712–57,324,672 | 52.2 kb | Distal (>10kb) Multiome | 392 | |
| chr15:57,372,267–57,372,459 | 4.0 kb | Proximal (<10kb) | 51 | |
| chr15:57,376,103–57,377,146 | 40 bp | At TSS Multiome | 482 | |
| chr15:57,382,704–57,383,499 | 6.7 kb | Proximal (<10kb) Multiome | 134 | |
| chr15:57,385,937–57,386,391 | 9.6 kb | Proximal (<10kb) Multiome | 106 | |
| chr15:57,411,681–57,412,959 | 35.9 kb | Distal (>10kb) Multiome | 165 | |
| chr15:57,477,799–57,478,810 | 101.8 kb | Distal (>10kb) Multiome | 603 | |
| chr15:57,495,641–57,496,411 | 119.6 kb | Distal (>10kb) Multiome | 71 | |
| chr15:57,501,832–57,502,700 | 125.7 kb | Distal (>10kb) Multiome | 59 | |
| chr15:57,591,431–57,592,312 | 215.4 kb | Distal (>10kb) Multiome | 318 |
Genomic view of the CGNL1 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.