This gene encodes a tumor suppressor protein that inhibits DNA synthesis and oncogenic transformation through association with the retinoblastoma 1 protein. The encoded protein also interacts with a complex of other cell cycle regulators to repress cell cycle-dependent gene expression in non-dividing cells. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene. [provided by RefSeq, Jul 2012]
Transcription factors with Perturb-seq knockdown data for LIN9. 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 = LIN9 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 LIN9, 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 |
|---|---|---|---|---|
| chr1:226,061,587–226,063,333 | 246.6 kb | Distal (>10kb) Multiome | 976 | |
| chr1:226,082,913–226,084,135 | 225.6 kb | Distal (>10kb) Multiome | 852 | |
| chr1:226,109,567–226,111,083 | 199.1 kb | Distal (>10kb) Multiome | 768 | |
| chr1:226,121,192–226,122,943 | 187.3 kb | Distal (>10kb) Multiome | 840 | |
| chr1:226,125,045–226,125,680 | 183.8 kb | Distal (>10kb) Multiome | 373 | |
| chr1:226,186,167–226,187,132 | 122.4 kb | Distal (>10kb) Multiome | 939 | |
| chr1:226,210,358–226,211,556 | 98.2 kb | Distal (>10kb) Multiome | 262 | |
| chr1:226,214,653–226,215,688 | 93.8 kb | Distal (>10kb) Multiome | 145 | |
| chr1:226,222,744–226,224,297 | 85.7 kb | Distal (>10kb) Multiome | 635 | |
| chr1:226,227,753–226,229,876 | 80.7 kb | Distal (>10kb) Multiome | 240 | |
| chr1:226,308,507–226,309,932 | 87 bp | At TSS Multiome | 915 | |
| chr1:226,404,588–226,405,519 | 96.0 kb | Distal (>10kb) Multiome | 185 | |
| chr1:226,407,433–226,408,738 | 99.0 kb | Distal (>10kb) Multiome | 894 | |
| chr1:226,413,963–226,414,602 | 105.1 kb | Distal (>10kb) Multiome | 41 | |
| chr1:226,548,271–226,549,075 | 239.6 kb | Distal (>10kb) Multiome | 269 | |
| chr1:226,608,563–226,609,002 | 299.6 kb | Distal (>10kb) Multiome | 148 |
Genomic view of the LIN9 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.