This gene is transcribed into multiple transcript variants, some of which may function as non-coding RNAs. One of the transcript variants encodes a putative short protein that is localized to the nucleus (PMID:25978564). Expression of this locus is increased in proliferating tissues, including certain tumors such as colorectal adenomas and adenocarcinomas. Transcription from this gene is negatively regulated by insulin and insulin-like growth factors, and may regulate the expression of genes involved in metabolism. [provided by RefSeq, May 2015]
Transcription factors with Perturb-seq knockdown data for CRNDE. 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 = CRNDE 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 CRNDE, 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 |
|---|---|---|---|---|
| chr16:54,199,531–54,200,186 | 729.4 kb | Distal (>10kb) Multiome HiCAR | 43 | |
| chr16:54,207,934–54,208,931 | 720.9 kb | Distal (>10kb) Multiome HiCAR | 181 | |
| chr16:54,211,232–54,211,931 | 717.6 kb | Distal (>10kb) Multiome HiCAR | 25 | |
| chr16:54,282,317–54,283,163 | 646.7 kb | Distal (>10kb) Multiome HiCAR | 207 | |
| chr16:54,283,950–54,287,988 | 642.3 kb | Distal (>10kb) Multiome HiCAR | 857 | |
| chr16:54,927,023–54,927,633 | 1.2 kb | Proximal (<10kb) | 212 | |
| chr16:54,927,769–54,931,725 | 22 bp | At TSS Multiome | 746 | |
| chr16:54,931,969–54,933,833 | 4.1 kb | Proximal (<10kb) Multiome | 172 | |
| chr16:54,934,833–54,935,237 | 6.0 kb | Proximal (<10kb) | 113 | |
| chr16:54,936,252–54,937,937 | 7.4 kb | Proximal (<10kb) | 276 | |
| chr16:54,938,325–54,938,703 | 9.5 kb | Proximal (<10kb) | 99 | |
| chr16:54,938,813–54,939,012 | 10.0 kb | Proximal (<10kb) | 60 | |
| chr16:55,056,580–55,057,535 | 127.7 kb | Distal (>10kb) Multiome | 230 | |
| chr16:55,167,660–55,168,195 | 238.8 kb | Distal (>10kb) Multiome | 147 |
Genomic view of the CRNDE 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.