This gene product is highly similar to Schizosaccharomyces pombe rad9, a cell cycle checkpoint protein required for cell cycle arrest and DNA damage repair. This protein possesses 3' to 5' exonuclease activity, which may contribute to its role in sensing and repairing DNA damage. It forms a checkpoint protein complex with RAD1 and HUS1. This complex is recruited by checkpoint protein RAD17 to the sites of DNA damage, which is thought to be important for triggering the checkpoint-signaling cascade. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Aug 2011]
Transcription factors with Perturb-seq knockdown data for RAD9A. 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 = RAD9A 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 RAD9A, 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 |
|---|---|---|---|---|
| chr11:67,023,002–67,023,688 | 294.4 kb | Distal (>10kb) Multiome | 243 | |
| chr11:67,056,596–67,057,312 | 261.0 kb | Distal (>10kb) Multiome | 382 | |
| chr11:67,071,470–67,071,999 | 246.1 kb | Distal (>10kb) Multiome HiCAR | 302 | |
| chr11:67,117,553–67,120,314 | 198.8 kb | Distal (>10kb) Multiome | 762 | |
| chr11:67,239,493–67,240,241 | 77.9 kb | Distal (>10kb) Multiome | 792 | |
| chr11:67,265,898–67,267,077 | 51.4 kb | Distal (>10kb) Multiome | 471 | |
| chr11:67,288,260–67,289,971 | 28.7 kb | Distal (>10kb) Multiome | 985 | |
| chr11:67,302,488–67,304,170 | 14.5 kb | Distal (>10kb) Multiome | 661 | |
| chr11:67,316,992–67,318,501 | 146 bp | At TSS Multiome | 918 | |
| chr11:67,352,967–67,354,228 | 35.8 kb | Distal (>10kb) Multiome | 781 | |
| chr11:67,372,171–67,373,596 | 55.2 kb | Distal (>10kb) Multiome | 497 | |
| chr11:67,373,784–67,374,410 | 1.6 kb | Proximal (<10kb) | 562 | |
| chr11:67,382,608–67,382,833 | 6.6 kb | Proximal (<10kb) | 375 | |
| chr11:67,391,276–67,392,428 | 74.0 kb | Distal (>10kb) Multiome | 957 | |
| chr11:67,401,038–67,402,351 | 84.0 kb | Distal (>10kb) Multiome | 741 | |
| chr11:67,420,418–67,421,666 | 103.4 kb | Distal (>10kb) Multiome | 648 | |
| chr11:67,428,036–67,428,950 | 110.5 kb | Distal (>10kb) Multiome | 813 | |
| chr11:67,443,182–67,444,063 | 125.8 kb | Distal (>10kb) Multiome | 612 | |
| chr11:67,464,410–67,465,252 | 146.9 kb | Distal (>10kb) Multiome | 710 | |
| chr11:67,468,551–67,469,666 | 151.4 kb | Distal (>10kb) Multiome | 774 | |
| chr11:67,482,830–67,483,745 | 165.3 kb | Distal (>10kb) Multiome | 969 | |
| chr11:67,504,073–67,506,408 | 188.5 kb | Distal (>10kb) Multiome | 769 | |
| chr11:67,507,504–67,509,030 | 190.5 kb | Distal (>10kb) Multiome | 897 | |
| chr11:67,583,474–67,584,777 | 265.9 kb | Distal (>10kb) Multiome | 633 | |
| chr11:67,606,302–67,607,213 | 289.0 kb | Distal (>10kb) Multiome | 781 | |
| chr11:67,614,064–67,614,626 | 296.4 kb | Distal (>10kb) Multiome | 383 | |
| chr11:67,619,429–67,620,391 | 302.0 kb | Distal (>10kb) Multiome | 50 | |
| chr11:67,628,876–67,631,242 | 312.5 kb | Distal (>10kb) Multiome | 1018 |
Genomic view of the RAD9A 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.