This gene is a member of the transformer 2 homolog family and encodes a protein with several RRM (RNA recognition motif) domains. This phosphorylated nuclear protein binds to specific RNA sequences and plays a role in the regulation of pre-mRNA splicing. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2013]
Transcription factors with Perturb-seq knockdown data for TRA2A. 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 = TRA2A 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 TRA2A, 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 |
|---|---|---|---|---|
| chr7:23,247,362–23,248,065 | 284.2 kb | Distal (>10kb) Multiome | 202 | |
| chr7:23,299,105–23,299,994 | 232.7 kb | Distal (>10kb) Multiome HiCAR | 852 | |
| chr7:23,465,333–23,465,840 | 66.5 kb | Distal (>10kb) Multiome | 410 | |
| chr7:23,470,190–23,471,917 | 60.7 kb | Distal (>10kb) Multiome | 922 | |
| chr7:23,473,588–23,475,134 | 57.5 kb | Distal (>10kb) Multiome | 996 | |
| chr7:23,528,702–23,528,886 | 3.1 kb | Proximal (<10kb) | 34 | |
| chr7:23,531,132–23,532,637 | 67 bp | At TSS Multiome | 1024 | |
| chr7:23,596,997–23,598,169 | 65.5 kb | Distal (>10kb) Multiome | 879 | |
| chr7:23,679,780–23,681,279 | 148.1 kb | Distal (>10kb) Multiome | 505 | |
| chr7:23,696,878–23,697,414 | 165.2 kb | Distal (>10kb) Multiome | 334 | |
| chr7:23,723,610–23,724,568 | 192.2 kb | Distal (>10kb) Multiome | 80 | |
| chr7:23,802,050–23,802,809 | 270.4 kb | Distal (>10kb) Multiome | 388 |
Genomic view of the TRA2A 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.