Involved in negative regulation of autophagosome assembly; negative regulation of autophagosome maturation; and positive regulation of viral genome replication. Located in endoplasmic reticulum membrane. [provided by Alliance of Genome Resources, Jul 2025]
Transcription factors with Perturb-seq knockdown data for TMEM39A. 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 = TMEM39A 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 TMEM39A, 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 |
|---|---|---|---|---|
| chr3:119,173,189–119,173,912 | 290.1 kb | Distal (>10kb) Multiome | 150 | |
| chr3:119,206,295–119,207,798 | 256.6 kb | Distal (>10kb) Multiome | 256 | |
| chr3:119,210,998–119,211,738 | 252.2 kb | Distal (>10kb) Multiome | 234 | |
| chr3:119,240,068–119,241,279 | 222.8 kb | Distal (>10kb) Multiome | 820 | |
| chr3:119,241,393–119,241,941 | 221.9 kb | Distal (>10kb) Multiome | 393 | |
| chr3:119,293,740–119,295,412 | 169.5 kb | Distal (>10kb) Multiome | 540 | |
| chr3:119,322,394–119,324,118 | 140.6 kb | Distal (>10kb) Multiome | 824 | |
| chr3:119,349,421–119,349,961 | 114.0 kb | Distal (>10kb) Multiome | 181 | |
| chr3:119,350,134–119,350,644 | 113.3 kb | Distal (>10kb) Multiome | 175 | |
| chr3:119,360,851–119,361,645 | 102.3 kb | Distal (>10kb) Multiome | 107 | |
| chr3:119,417,868–119,418,544 | 45.3 kb | Distal (>10kb) Multiome | 156 | |
| chr3:119,463,124–119,464,243 | 62 bp | At TSS Multiome | 902 | |
| chr3:119,468,550–119,469,486 | 5.4 kb | Proximal (<10kb) Multiome | 832 | |
| chr3:119,497,916–119,499,024 | 34.9 kb | Distal (>10kb) Multiome | 886 | |
| chr3:119,579,336–119,580,732 | 116.3 kb | Distal (>10kb) Multiome | 519 | |
| chr3:119,676,820–119,677,853 | 213.7 kb | Distal (>10kb) Multiome | 778 | |
| chr3:119,702,500–119,703,521 | 239.4 kb | Distal (>10kb) Multiome | 399 |
Genomic view of the TMEM39A 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.