This gene belongs to the chemokine-like factor gene superfamily, a novel family that is similar to the chemokine and the transmembrane 4 superfamilies of signaling molecules. This gene is one of several chemokine-like factor genes located in a cluster on chromosome 16. Alternatively spliced transcript variants containing different 5' UTRs, but encoding the same protein, have been identified. [provided by RefSeq, Jul 2008]
Transcription factors with Perturb-seq knockdown data for CMTM3. 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 = CMTM3 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 CMTM3, 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 |
|---|---|---|---|---|
| chr16:66,406,327–66,407,221 | 197.1 kb | Distal (>10kb) Multiome | 614 | |
| chr16:66,426,889–66,427,792 | 176.6 kb | Distal (>10kb) Multiome | 269 | |
| chr16:66,433,312–66,434,244 | 170.1 kb | Distal (>10kb) Multiome | 678 | |
| chr16:66,549,337–66,550,427 | 54.0 kb | Distal (>10kb) Multiome | 817 | |
| chr16:66,552,056–66,553,030 | 51.3 kb | Distal (>10kb) Multiome | 994 | |
| chr16:66,603,736–66,605,778 | 797 bp | At TSS Multiome | 907 | |
| chr16:66,608,358–66,609,044 | 4.8 kb | Proximal (<10kb) Multiome | 698 | |
| chr16:66,616,501–66,617,327 | 13.0 kb | Distal (>10kb) Multiome | 204 | |
| chr16:66,695,775–66,697,411 | 93.0 kb | Distal (>10kb) Multiome | 714 | |
| chr16:66,751,110–66,752,176 | 147.9 kb | Distal (>10kb) Multiome | 734 | |
| chr16:66,830,425–66,831,324 | 227.0 kb | Distal (>10kb) Multiome | 934 | |
| chr16:66,844,097–66,844,861 | 240.6 kb | Distal (>10kb) Multiome | 211 | |
| chr16:66,872,965–66,873,714 | 269.4 kb | Distal (>10kb) Multiome | 836 | |
| chr16:66,880,003–66,881,270 | 276.6 kb | Distal (>10kb) Multiome | 1020 |
Genomic view of the CMTM3 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.