This gene encodes a type III intermediate filament protein. Intermediate filaments, along with microtubules and actin microfilaments, make up the cytoskeleton. The encoded protein is responsible for maintaining cell shape and integrity of the cytoplasm, and stabilizing cytoskeletal interactions. This protein is involved in neuritogenesis and cholesterol transport and functions as an organizer of a number of other critical proteins involved in cell attachment, migration, and signaling. Bacterial and viral pathogens have been shown to attach to this protein on the host cell surface. Mutations in this gene are associated with congenital cataracts in human patients. [provided by RefSeq, Aug 2017]
Transcription factors with Perturb-seq knockdown data for VIM. 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 = VIM 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 VIM, 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 |
|---|---|---|---|---|
| chr10:15,856,555–15,857,325 | 1372.4 kb | Distal (>10kb) Multiome HiCAR | 264 | |
| chr10:16,891,324–16,892,326 | 337.6 kb | Distal (>10kb) Multiome HiCAR | 599 | |
| chr10:16,962,424–16,962,891 | 266.6 kb | Distal (>10kb) Multiome | 31 | |
| chr10:17,200,899–17,202,136 | 27.7 kb | Distal (>10kb) Multiome | 1040 | |
| chr10:17,228,175–17,230,908 | 261 bp | At TSS Multiome | 920 | |
| chr10:17,379,036–17,380,059 | 150.2 kb | Distal (>10kb) Multiome | 120 | |
| chr10:17,387,758–17,388,950 | 159.0 kb | Distal (>10kb) Multiome | 319 | |
| chr10:17,453,122–17,455,034 | 225.1 kb | Distal (>10kb) Multiome | 584 |
Genomic view of the VIM 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.