The protein encoded by this gene is a member of the protein tyrosine phosphatase (PTP) family. PTPs are known to be signaling molecules that regulate a variety of cellular processes including cell growth, differentiation, mitotic cycle, and oncogenic transformation. This PTP possesses an extracellular region, a single transmembrane region, and two tandem intracytoplasmic catalytic domains, and thus represents a receptor-type PTP. The extracellular region contains three Ig-like domains, and nine non-Ig like domains similar to that of neural-cell adhesion molecule. This PTP was shown to function in the regulation of epithelial cell-cell contacts at adherents junctions, as well as in the control of beta-catenin signaling. An increased expression level of this protein was found in the insulin-responsive tissue of obese, insulin-resistant individuals, and may contribute to the pathogenesis of insulin resistance. Two alternatively spliced transcript variants of this gene, which encode distinct proteins, have been reported. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PTPRF. 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 = PTPRF 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 PTPRF, 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 |
|---|---|---|---|---|
| chr1:43,270,344–43,271,458 | 260.1 kb | Distal (>10kb) Multiome | 301 | |
| chr1:43,285,284–43,285,996 | 245.2 kb | Distal (>10kb) Multiome | 403 | |
| chr1:43,348,408–43,350,097 | 181.6 kb | Distal (>10kb) Multiome | 819 | |
| chr1:43,358,112–43,359,560 | 172.0 kb | Distal (>10kb) Multiome | 818 | |
| chr1:43,366,277–43,366,800 | 164.4 kb | Distal (>10kb) Multiome | 226 | |
| chr1:43,366,988–43,368,619 | 162.7 kb | Distal (>10kb) Multiome | 991 | |
| chr1:43,389,284–43,390,213 | 141.1 kb | Distal (>10kb) Multiome | 905 | |
| chr1:43,452,851–43,454,257 | 77.5 kb | Distal (>10kb) Multiome | 455 | |
| chr1:43,454,433–43,454,997 | 76.2 kb | Distal (>10kb) Multiome | 267 | |
| chr1:43,529,225–43,529,452 | 1.4 kb | Proximal (<10kb) | 368 | |
| chr1:43,530,512–43,532,007 | 62 bp | At TSS Multiome | 520 | |
| chr1:43,545,657–43,546,353 | 15.1 kb | Distal (>10kb) Multiome | 445 | |
| chr1:43,549,934–43,550,659 | 19.4 kb | Distal (>10kb) Multiome | 343 | |
| chr1:43,565,502–43,566,158 | 34.9 kb | Distal (>10kb) Multiome | 173 | |
| chr1:43,649,463–43,650,795 | 119.3 kb | Distal (>10kb) Multiome | 997 | |
| chr1:43,707,108–43,708,162 | 176.7 kb | Distal (>10kb) Multiome | 937 |
Genomic view of the PTPRF 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.