This gene encodes a protein that functions in multiple regulatory pathways. The encoded protein complexes with numerous cytosolic proteins and performs diverse functions including regulation of small nuclear ribonucleoprotein biosynthesis, platelet activation and cytoskeletal organization. The protein is also found associated with the plasma membrane where it functions as a chloride current regulator. Pseudogenes of this gene are found on chromosomes 1, 4 and 6. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2015]
Transcription factors with Perturb-seq knockdown data for CLNS1A. 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 = CLNS1A 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 CLNS1A, 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 |
|---|---|---|---|---|
| chr11:77,171,758–77,172,392 | 465.7 kb | Distal (>10kb) Multiome HiCAR | 275 | |
| chr11:77,191,860–77,192,374 | 445.6 kb | Distal (>10kb) Multiome HiCAR | 447 | |
| chr11:77,411,314–77,412,382 | 225.8 kb | Distal (>10kb) Multiome | 405 | |
| chr11:77,436,791–77,437,318 | 200.6 kb | Distal (>10kb) Multiome | 44 | |
| chr11:77,473,004–77,474,837 | 163.6 kb | Distal (>10kb) Multiome | 769 | |
| chr11:77,555,382–77,556,090 | 82.0 kb | Distal (>10kb) Multiome | 138 | |
| chr11:77,589,259–77,590,628 | 48.0 kb | Distal (>10kb) Multiome | 830 | |
| chr11:77,637,444–77,638,090 | 35 bp | At TSS Multiome | 929 | |
| chr11:77,819,354–77,821,704 | 183.2 kb | Distal (>10kb) Multiome | 1047 |
Genomic view of the CLNS1A 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.