Cell signaling pathways rely on a dynamic interaction between activating and inhibiting processes. SHP-1-mediated dephosphorylation of protein tyrosine residues is central to the regulation of several cell signaling pathways. Two types of inhibitory receptor superfamily members are immunoreceptor tyrosine-based inhibitory motif (ITIM)-bearing receptors and their non-ITIM-bearing, activating counterparts. Control of cell signaling via SHP-1 is thought to occur through a balance between PILRalpha-mediated inhibition and PILRbeta-mediated activation. These paired immunoglobulin-like receptor genes are located in a tandem head-to-tail orientation on chromosome 7. This particular gene encodes the ITIM-bearing member of the receptor pair, which functions in the inhibitory role. Alternative splicing has been observed at this locus and three variants, each encoding a distinct isoform, are described. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for PILRA. 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 = PILRA 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 PILRA, 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 |
|---|---|---|---|---|
| chr7:100,081,134–100,083,000 | 292.2 kb | Distal (>10kb) Multiome | 1160 | |
| chr7:100,088,454–100,089,460 | 285.1 kb | Distal (>10kb) Multiome | 955 | |
| chr7:100,100,270–100,102,380 | 273.4 kb | Distal (>10kb) Multiome | 1102 | |
| chr7:100,119,029–100,120,415 | 254.5 kb | Distal (>10kb) Multiome | 954 | |
| chr7:100,126,675–100,128,006 | 246.8 kb | Distal (>10kb) Multiome | 919 | |
| chr7:100,148,262–100,149,663 | 225.2 kb | Distal (>10kb) Multiome | 846 | |
| chr7:100,158,247–100,159,079 | 215.3 kb | Distal (>10kb) Multiome | 795 | |
| chr7:100,167,090–100,167,783 | 206.6 kb | Distal (>10kb) Multiome | 123 | |
| chr7:100,167,894–100,168,793 | 205.4 kb | Distal (>10kb) Multiome | 439 | |
| chr7:100,171,153–100,171,887 | 202.6 kb | Distal (>10kb) Multiome | 233 | |
| chr7:100,176,986–100,178,152 | 196.5 kb | Distal (>10kb) Multiome | 626 | |
| chr7:100,266,531–100,267,045 | 107.3 kb | Distal (>10kb) Multiome | 24 | |
| chr7:100,270,225–100,270,813 | 103.4 kb | Distal (>10kb) Multiome | 103 | |
| chr7:100,271,732–100,272,774 | 101.7 kb | Distal (>10kb) Multiome | 530 | |
| chr7:100,335,652–100,336,470 | 37.9 kb | Distal (>10kb) Multiome | 706 | |
| chr7:100,381,682–100,382,670 | 8.0 kb | Proximal (<10kb) Multiome | 49 | |
| chr7:100,428,059–100,431,175 | 54.9 kb | Distal (>10kb) Multiome | 1296 | |
| chr7:100,435,379–100,436,927 | 62.5 kb | Distal (>10kb) Multiome | 931 | |
| chr7:100,450,379–100,450,973 | 76.7 kb | Distal (>10kb) Multiome | 785 | |
| chr7:100,478,582–100,479,753 | 105.3 kb | Distal (>10kb) Multiome | 842 | |
| chr7:100,482,937–100,484,533 | 109.6 kb | Distal (>10kb) Multiome | 677 | |
| chr7:100,538,557–100,539,759 | 165.0 kb | Distal (>10kb) Multiome | 858 | |
| chr7:100,542,221–100,542,986 | 168.6 kb | Distal (>10kb) Multiome | 274 | |
| chr7:100,569,177–100,570,642 | 195.6 kb | Distal (>10kb) Multiome | 855 | |
| chr7:100,585,161–100,587,241 | 212.3 kb | Distal (>10kb) Multiome | 966 | |
| chr7:100,611,685–100,612,981 | 238.2 kb | Distal (>10kb) Multiome | 767 | |
| chr7:100,626,427–100,627,057 | 252.7 kb | Distal (>10kb) Multiome | 415 | |
| chr7:100,656,111–100,656,626 | 282.4 kb | Distal (>10kb) Multiome | 653 | |
| chr7:100,673,043–100,674,892 | 299.5 kb | Distal (>10kb) Multiome | 934 |
Genomic view of the PILRA 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.