This protein encoded by this gene localizes to the nucleus and is expressed in numerous tissues including brain, testis, liver, and kidney. This refseq contains genomic sequence in its 3' UTR which is not supported by experimental evidence. Computer predictions indicate that this region of the 3' UTR contains hairpin-forming self-complementary sequence which is possibly excised after transcription. This gene has a pseudogene on chromosome X. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for NICN1. 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 = NICN1 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 NICN1, 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 |
|---|---|---|---|---|
| chr3:49,132,603–49,133,965 | 295.6 kb | Distal (>10kb) Multiome | 652 | |
| chr3:49,166,057–49,166,586 | 263.0 kb | Distal (>10kb) Multiome HiCAR | 622 | |
| chr3:49,170,896–49,171,950 | 257.9 kb | Distal (>10kb) Multiome | 781 | |
| chr3:49,276,912–49,277,398 | 152.2 kb | Distal (>10kb) Multiome | 291 | |
| chr3:49,339,607–49,340,853 | 89.1 kb | Distal (>10kb) Multiome HiCAR | 1044 | |
| chr3:49,357,868–49,359,083 | 70.8 kb | Distal (>10kb) Multiome | 908 | |
| chr3:49,411,409–49,412,844 | 17.1 kb | Distal (>10kb) Multiome | 899 | |
| chr3:49,422,179–49,422,905 | 6.8 kb | Proximal (<10kb) Multiome | 453 | |
| chr3:49,428,857–49,429,869 | 169 bp | At TSS Multiome | 712 | |
| chr3:49,468,926–49,470,930 | 40.9 kb | Distal (>10kb) Multiome | 919 | |
| chr3:49,539,369–49,540,584 | 110.7 kb | Distal (>10kb) Multiome | 628 | |
| chr3:49,553,618–49,555,244 | 125.2 kb | Distal (>10kb) Multiome | 710 | |
| chr3:49,718,116–49,720,106 | 290.3 kb | Distal (>10kb) Multiome | 450 | |
| chr3:49,723,361–49,724,517 | 294.8 kb | Distal (>10kb) Multiome | 769 |
Genomic view of the NICN1 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.