This gene belongs to a small gene family whose members have an N-terminal VHS domain followed by a GAT domain; domains which typically participate in vesicular trafficking. The canonical protein encoded by this gene also has a C-terminal clathrin binding motif. This protein has been shown to interact with Tollip, clathrin and ubiquitin and is thought to play a role in endosomal sorting. This gene resides in the 3.7 Mb deletion of chromosome region 17p11.2 that is associated with Smith-Magenis syndrome. Alternative splicing results in multiple transcript variants encoding distinct proteins. [provided by RefSeq, Apr 2017]
Transcription factors with Perturb-seq knockdown data for TOM1L2. 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 = TOM1L2 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 TOM1L2, 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 |
|---|---|---|---|---|
| chr17:17,680,744–17,682,037 | 291.1 kb | Distal (>10kb) Multiome | 507 | |
| chr17:17,682,791–17,683,426 | 289.4 kb | Distal (>10kb) Multiome | 510 | |
| chr17:17,693,050–17,694,108 | 279.0 kb | Distal (>10kb) Multiome | 549 | |
| chr17:17,694,284–17,695,355 | 277.6 kb | Distal (>10kb) Multiome | 703 | |
| chr17:17,700,114–17,700,885 | 271.9 kb | Distal (>10kb) Multiome | 327 | |
| chr17:17,724,458–17,725,494 | 247.4 kb | Distal (>10kb) Multiome | 283 | |
| chr17:17,751,962–17,752,874 | 220.1 kb | Distal (>10kb) Multiome | 640 | |
| chr17:17,780,889–17,783,985 | 191.3 kb | Distal (>10kb) Multiome | 655 | |
| chr17:17,792,432–17,793,087 | 179.6 kb | Distal (>10kb) Multiome | 135 | |
| chr17:17,809,458–17,811,066 | 162.4 kb | Distal (>10kb) Multiome | 371 | |
| chr17:17,811,471–17,812,921 | 160.0 kb | Distal (>10kb) Multiome | 664 | |
| chr17:17,823,156–17,824,542 | 148.6 kb | Distal (>10kb) Multiome | 743 | |
| chr17:17,835,765–17,838,695 | 136.1 kb | Distal (>10kb) Multiome | 1030 | |
| chr17:17,839,788–17,841,046 | 132.2 kb | Distal (>10kb) Multiome | 927 | |
| chr17:17,921,363–17,921,988 | 50.7 kb | Distal (>10kb) Multiome | 341 | |
| chr17:17,943,271–17,943,954 | 28.9 kb | Distal (>10kb) Multiome | 143 | |
| chr17:17,965,260–17,965,665 | 6.8 kb | Proximal (<10kb) | 25 | |
| chr17:17,971,984–17,973,164 | 212 bp | At TSS Multiome | 716 | |
| chr17:18,035,659–18,036,594 | 63.6 kb | Distal (>10kb) Multiome | 186 | |
| chr17:18,038,656–18,040,279 | 66.9 kb | Distal (>10kb) Multiome | 839 | |
| chr17:18,153,365–18,154,352 | 181.5 kb | Distal (>10kb) Multiome | 244 | |
| chr17:18,157,790–18,158,725 | 185.8 kb | Distal (>10kb) Multiome | 292 | |
| chr17:18,182,585–18,185,065 | 211.1 kb | Distal (>10kb) Multiome | 1051 | |
| chr17:18,224,148–18,226,173 | 252.3 kb | Distal (>10kb) Multiome | 680 | |
| chr17:18,246,777–18,247,912 | 274.9 kb | Distal (>10kb) Multiome | 314 | |
| chr17:18,257,865–18,259,083 | 286.2 kb | Distal (>10kb) Multiome | 684 | |
| chr17:18,260,145–18,261,582 | 288.2 kb | Distal (>10kb) Multiome | 778 |
Genomic view of the TOM1L2 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.