This gene encodes a member of the metallo-beta-lactamase family. The encoded protein is a 73kDa subunit of the cleavage and polyadenylation specificity factor and functions as an endonuclease that recognizes the pre-mRNA 3'-cleavage site AAUAAA prior to polyadenylation. It also cleaves after the pre-mRNA sequence ACCCA during histone 3'-end pre-mRNA processing. [provided by RefSeq, Oct 2012]
Transcription factors with Perturb-seq knockdown data for CPSF3. 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 = CPSF3 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 CPSF3, 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 |
|---|---|---|---|---|
| chr2:9,142,361–9,143,365 | 280.8 kb | Distal (>10kb) Multiome HiCAR | 712 | |
| chr2:9,177,942–9,178,829 | 245.2 kb | Distal (>10kb) Multiome | 196 | |
| chr2:9,205,968–9,208,238 | 217.0 kb | Distal (>10kb) Multiome | 800 | |
| chr2:9,218,015–9,218,554 | 205.5 kb | Distal (>10kb) Multiome | 107 | |
| chr2:9,422,555–9,424,057 | 133 bp | At TSS Multiome | 1016 | |
| chr2:9,473,505–9,475,238 | 51.1 kb | Distal (>10kb) Multiome | 602 | |
| chr2:9,475,498–9,477,288 | 53.1 kb | Distal (>10kb) Multiome | 228 | |
| chr2:9,554,934–9,556,567 | 132.2 kb | Distal (>10kb) Multiome | 1091 | |
| chr2:9,630,002–9,631,663 | 207.4 kb | Distal (>10kb) Multiome | 995 |
Genomic view of the CPSF3 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.