This gene belongs to the signal induced proliferation associated 1 family of genes, which encode GTPase-activating proteins specific for the GTP-binding protein Rap1. Rap1 has been implicated in regulation of cell adhesion, cell polarity, and organization of the cytoskeleton. Like other members of the family, the protein encoded by this gene contains RapGAP and PDZ domains. In addition, this protein contains a C-terminal leucine zipper domain. This gene is proposed to function in epithelial cell morphogenesis and establishment or maintenance of polarity. Consistently, expression of the protein in cell culture showed localization to cell-cell borders in apical regions, and downregulation of the gene in 3D Caco2 cell culture resulted in abnormal cell polarity and morphogenesis. Allelic variants of this gene have been associated with congenital cataracts in humans. [provided by RefSeq, Feb 2016]
Transcription factors with Perturb-seq knockdown data for SIPA1L3. 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 = SIPA1L3 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 SIPA1L3, 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 |
|---|---|---|---|---|
| chr19:37,654,736–37,656,463 | 251.5 kb | Distal (>10kb) Multiome | 1001 | |
| chr19:37,691,873–37,692,535 | 214.9 kb | Distal (>10kb) Multiome | 609 | |
| chr19:37,719,078–37,720,106 | 187.5 kb | Distal (>10kb) Multiome | 698 | |
| chr19:37,779,176–37,780,039 | 127.5 kb | Distal (>10kb) Multiome | 808 | |
| chr19:37,902,652–37,902,911 | 4.3 kb | Proximal (<10kb) | 235 | |
| chr19:37,906,047–37,907,698 | 339 bp | At TSS Multiome | 915 | |
| chr19:38,004,389–38,004,823 | 97.5 kb | Distal (>10kb) Multiome | 367 | |
| chr19:38,043,611–38,044,643 | 136.6 kb | Distal (>10kb) Multiome HiCAR | 66 | |
| chr19:38,074,116–38,074,898 | 167.3 kb | Distal (>10kb) Multiome HiCAR | 299 | |
| chr19:38,183,265–38,183,970 | 276.4 kb | Distal (>10kb) Multiome HiCAR | 156 | |
| chr19:38,223,967–38,224,571 | 317.1 kb | Distal (>10kb) Multiome HiCAR | 677 | |
| chr19:38,229,570–38,230,021 | 322.6 kb | Distal (>10kb) Multiome HiCAR | 354 |
Genomic view of the SIPA1L3 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.