This gene is a member of the neuroblastoma breakpoint family (NBPF) which consists of dozens of recently duplicated genes primarily located in segmental duplications on human chromosome 1. This gene family has experienced its greatest expansion within the human lineage and has expanded, to a lesser extent, among primates in general. Members of this gene family are characterized by tandemly repeated copies of DUF1220 protein domains. DUF1220 copy number variations in human chromosomal region 1q21.1, where most DUF1220 domains are located, have been implicated in a number of developmental and neurogenetic diseases such as microcephaly, macrocephaly, autism, schizophrenia, cognitive disability, congenital heart disease, neuroblastoma, and congenital kidney and urinary tract anomalies. Altered expression of some gene family members is associated with several types of cancer. This gene family contains numerous pseudogenes. [provided by RefSeq, Feb 2013]
Transcription factors with Perturb-seq knockdown data for NBPF3. 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 = NBPF3 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 NBPF3, 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 |
|---|---|---|---|---|
| chr1:21,175,743–21,177,594 | 263.1 kb | Distal (>10kb) Multiome | 807 | |
| chr1:21,289,691–21,290,756 | 150.1 kb | Distal (>10kb) Multiome | 389 | |
| chr1:21,344,857–21,346,026 | 94.5 kb | Distal (>10kb) Multiome | 850 | |
| chr1:21,436,521–21,437,523 | 3.1 kb | Proximal (<10kb) Multiome | 100 | |
| chr1:21,439,762–21,440,452 | 22 bp | At TSS Multiome | 454 | |
| chr1:21,490,894–21,491,460 | 50.9 kb | Distal (>10kb) Multiome | 154 | |
| chr1:21,491,962–21,492,562 | 52.2 kb | Distal (>10kb) Multiome | 116 | |
| chr1:21,497,823–21,498,256 | 58.0 kb | Distal (>10kb) Multiome | 85 | |
| chr1:21,508,855–21,510,512 | 70.3 kb | Distal (>10kb) Multiome | 399 | |
| chr1:21,607,576–21,608,530 | 167.8 kb | Distal (>10kb) Multiome | 338 | |
| chr1:21,621,983–21,623,132 | 182.4 kb | Distal (>10kb) Multiome | 228 | |
| chr1:21,638,784–21,640,464 | 199.7 kb | Distal (>10kb) Multiome | 542 | |
| chr1:21,651,625–21,652,424 | 211.8 kb | Distal (>10kb) Multiome | 367 | |
| chr1:21,659,145–21,659,637 | 219.3 kb | Distal (>10kb) Multiome | 960 | |
| chr1:21,668,987–21,670,050 | 229.3 kb | Distal (>10kb) Multiome | 743 |
Genomic view of the NBPF3 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.