The protein encoded by this gene is a transcriptional regulator that binds as a homodimer to activating transcription factor (ATF) sites in many cellular and viral promoters. The encoded protein represses PER1 and PER2 expression and therefore plays a role in the regulation of circadian rhythm. Three transcript variants encoding the same protein have been found for this gene. [provided by RefSeq, Feb 2014]
Transcription factors with Perturb-seq knockdown data for NFIL3. 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 = NFIL3 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 NFIL3, 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 |
|---|---|---|---|---|
| chr9:91,036,858–91,037,648 | 386.5 kb | Distal (>10kb) Multiome HiCAR | 720 | |
| chr9:91,193,714–91,194,128 | 230.1 kb | Distal (>10kb) Multiome | 920 | |
| chr9:91,361,213–91,362,454 | 61.9 kb | Distal (>10kb) Multiome | 745 | |
| chr9:91,421,095–91,421,758 | 2.4 kb | Proximal (<10kb) Multiome | 317 | |
| chr9:91,423,067–91,424,819 | 92 bp | At TSS Multiome | 822 | |
| chr9:91,714,355–91,714,808 | 290.8 kb | Distal (>10kb) Multiome | 186 | |
| chr9:91,721,275–91,721,895 | 297.6 kb | Distal (>10kb) Multiome | 91 |
Genomic view of the NFIL3 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.