This gene encodes a member of the NimA (never in mitosis A) family of serine/threonine protein kinases. The encoded protein differs from other NimA family members in that it is not cell cycle regulated and is found primarily in the cytoplasm. The kinase is activated by prolactin stimulation, leading to phosphorylation of VAV2 guanine nucleotide exchange factor, paxillin, and activation of the RAC1 GTPase. Two functional alleles for this gene have been identified in humans. The reference genome assembly (GRCh38) represents a functional allele that is associated with the inclusion of an additional coding exon in protein-coding transcripts, compared to an alternate functional allele that lacks the exon. [provided by RefSeq, Sep 2019]
Transcription factors with Perturb-seq knockdown data for NEK3. 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 = NEK3 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 NEK3, 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 |
|---|---|---|---|---|
| chr13:51,997,545–51,998,310 | 161.5 kb | Distal (>10kb) Multiome | 461 | |
| chr13:52,011,124–52,012,698 | 147.4 kb | Distal (>10kb) Multiome | 960 | |
| chr13:52,128,284–52,129,389 | 30.5 kb | Distal (>10kb) Multiome | 598 | |
| chr13:52,158,918–52,159,048 | 511 bp | At TSS | 214 | |
| chr13:52,159,155–52,160,117 | 1 bp | At TSS Multiome | 831 | |
| chr13:52,194,155–52,194,839 | 34.9 kb | Distal (>10kb) Multiome | 888 | |
| chr13:52,195,279–52,195,948 | 36.1 kb | Distal (>10kb) Multiome | 267 | |
| chr13:52,449,904–52,451,090 | 291.1 kb | Distal (>10kb) Multiome HiCAR | 972 | |
| chr13:52,454,948–52,456,258 | 295.9 kb | Distal (>10kb) Multiome HiCAR | 791 |
Genomic view of the NEK3 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.