This gene encodes an RNA methyltransferase which belongs to the rossmann fold methyltransferase family, and serves as a 5'-methylphosphate capping enzyme that is specific for cytoplasmic histidyl tRNA. The encoded protein contains an S-adenosylmethionine binding domain and uses the methyl group donor, S-adenosylmethionine. This gene is overexpressed in breast cancer cells, and is related to the tumorigenic phenotype and poor prognosis of breast cancer. The encoded protein is thought to promote the cellular invasion of breast cancer cells, by downregulating the expression of tumor suppressor miRNAs through the dimethylation of the 5-monophosphate of the corresponding precursor miRNAs. [provided by RefSeq, Apr 2017]
Transcription factors with Perturb-seq knockdown data for BCDIN3D. 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 = BCDIN3D 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 BCDIN3D, 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 |
|---|---|---|---|---|
| chr12:49,550,509–49,551,225 | 292.1 kb | Distal (>10kb) Multiome | 126 | |
| chr12:49,567,505–49,568,696 | 275.0 kb | Distal (>10kb) Multiome | 807 | |
| chr12:49,622,768–49,624,150 | 219.6 kb | Distal (>10kb) Multiome | 788 | |
| chr12:49,706,780–49,708,002 | 135.5 kb | Distal (>10kb) Multiome | 854 | |
| chr12:49,741,069–49,742,357 | 101.6 kb | Distal (>10kb) Multiome | 980 | |
| chr12:49,827,122–49,829,288 | 14.6 kb | Distal (>10kb) Multiome HiCAR | 839 | |
| chr12:49,842,401–49,843,296 | 71 bp | At TSS Multiome | 806 | |
| chr12:49,866,994–49,867,580 | 24.2 kb | Distal (>10kb) Multiome HiCAR | 334 | |
| chr12:49,945,408–49,945,886 | 102.6 kb | Distal (>10kb) Multiome | 520 | |
| chr12:49,961,271–49,962,190 | 118.6 kb | Distal (>10kb) Multiome | 164 | |
| chr12:49,966,854–49,967,924 | 124.3 kb | Distal (>10kb) Multiome | 698 | |
| chr12:50,024,956–50,025,990 | 182.4 kb | Distal (>10kb) Multiome | 829 | |
| chr12:50,050,458–50,051,443 | 207.8 kb | Distal (>10kb) Multiome | 412 | |
| chr12:50,057,263–50,058,231 | 214.6 kb | Distal (>10kb) Multiome | 437 | |
| chr12:50,084,798–50,085,859 | 242.2 kb | Distal (>10kb) Multiome | 715 | |
| chr12:50,110,765–50,112,744 | 268.9 kb | Distal (>10kb) Multiome | 967 |
Genomic view of the BCDIN3D 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.