This gene encodes a double zinc finger motif-containing protein that participates in the transforming growth factor-beta (TGFB) signalling pathway. The encoded protein interacts directly with SMAD2 and SMAD3, and recruits SMAD2 to the TGFB receptor. There are multiple pseudogenes for this gene on chromosomes 2, 15, and X. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2013]
Transcription factors with Perturb-seq knockdown data for ZFYVE9. 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 = ZFYVE9 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 ZFYVE9, 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 |
|---|---|---|---|---|
| chr1:51,877,934–51,879,493 | 263.2 kb | Distal (>10kb) Multiome | 1012 | |
| chr1:51,957,425–51,958,172 | 184.3 kb | Distal (>10kb) Multiome | 194 | |
| chr1:51,960,124–51,960,875 | 181.6 kb | Distal (>10kb) Multiome | 141 | |
| chr1:51,989,938–51,991,038 | 151.4 kb | Distal (>10kb) Multiome | 410 | |
| chr1:52,032,841–52,033,969 | 108.4 kb | Distal (>10kb) Multiome | 829 | |
| chr1:52,054,893–52,057,012 | 85.7 kb | Distal (>10kb) Multiome | 1080 | |
| chr1:52,141,669–52,142,926 | 12 bp | At TSS Multiome | 839 | |
| chr1:52,240,504–52,241,012 | 98.7 kb | Distal (>10kb) Multiome | 110 | |
| chr1:52,365,194–52,367,305 | 224.2 kb | Distal (>10kb) Multiome | 969 | |
| chr1:52,368,430–52,369,016 | 226.5 kb | Distal (>10kb) Multiome | 340 | |
| chr1:52,403,732–52,405,027 | 262.4 kb | Distal (>10kb) Multiome | 789 |
Genomic view of the ZFYVE9 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.