Quality control in the endoplasmic reticulum (ER) ensures that only properly folded proteins are retained in the cell through recognition and degradation of misfolded or unassembled proteins. EDEM3 belongs to a group of proteins that accelerate degradation of misfolded glycoproteins in the ER (Hirao et al., 2006 [PubMed 16431915]).[supplied by OMIM, Mar 2008]
Transcription factors with Perturb-seq knockdown data for EDEM3. 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 = EDEM3 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 EDEM3, 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 |
|---|---|---|---|---|
| chr1:184,582,004–184,583,178 | 172.4 kb | Distal (>10kb) Multiome | 114 | |
| chr1:184,663,783–184,664,949 | 90.7 kb | Distal (>10kb) Multiome | 369 | |
| chr1:184,695,922–184,696,742 | 58.5 kb | Distal (>10kb) Multiome | 40 | |
| chr1:184,754,064–184,755,736 | 146 bp | At TSS Multiome | 971 | |
| chr1:184,905,067–184,906,277 | 150.9 kb | Distal (>10kb) Multiome | 314 | |
| chr1:184,973,585–184,974,868 | 219.3 kb | Distal (>10kb) Multiome | 731 | |
| chr1:185,044,828–185,046,417 | 290.6 kb | Distal (>10kb) Multiome | 816 | |
| chr1:185,156,218–185,158,419 | 402.3 kb | Distal (>10kb) Multiome HiCAR | 949 |
Genomic view of the EDEM3 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.