VCL

vinculin | VINC

Vinculin is a cytoskeletal protein associated with cell-cell and cell-matrix junctions, where it is thought to function as one of several interacting proteins involved in anchoring F-actin to the membrane. Defects in VCL are the cause of cardiomyopathy dilated type 1W. Dilated cardiomyopathy is a disorder characterized by ventricular dilation and impaired systolic function, resulting in congestive heart failure and arrhythmia. Multiple alternatively spliced transcript variants have been found for this gene, but the biological validity of some variants has not been determined. [provided by RefSeq, Jul 2008]

Member of: DE-4 DE-4.26 Developmental clusters: GC1

Biological processes 77 terms

actin binding (GO:0003779)actin binding (GO:0003779)actin cytoskeleton (GO:0015629)adherens junction (GO:0005912)adherens junction (GO:0005912)adherens junction (GO:0005912)adherens junction (GO:0005912)adherens junction assembly (GO:0034333)alpha-catenin binding (GO:0045294)alpha-catenin binding (GO:0045294)apical junction assembly (GO:0043297)beta-catenin binding (GO:0008013)beta-catenin binding (GO:0008013)brush border (GO:0005903)cadherin binding (GO:0045296)cadherin binding (GO:0045296)cell adhesion (GO:0007155)cell adhesion (GO:0007155)cell adhesion (GO:0007155)cell-cell contact zone (GO:0044291)cell-cell contact zone (GO:0044291)cell-cell contact zone (GO:0044291)cell-cell junction (GO:0005911)cell-cell junction (GO:0005911)cell-matrix adhesion (GO:0007160)cell-substrate junction (GO:0030055)costamere (GO:0043034)costamere (GO:0043034)cytoplasm (GO:0005737)cytoskeleton (GO:0005856)cytoskeleton (GO:0005856)cytoskeleton (GO:0005856)cytosol (GO:0005829)dystroglycan binding (GO:0002162)epithelial cell-cell adhesion (GO:0090136)extracellular exosome (GO:0070062)extracellular region (GO:0005576)extracellular vesicle (GO:1903561)ficolin-1-rich granule lumen (GO:1904813)focal adhesion (GO:0005925)focal adhesion (GO:0005925)focal adhesion (GO:0005925)focal adhesion (GO:0005925)focal adhesion (GO:0005925)focal adhesion (GO:0005925)inner dense plaque of desmosome (GO:0090637)lamellipodium assembly (GO:0030032)maintenance of blood-brain barrier (GO:0035633)membrane (GO:0016020)membrane raft (GO:0045121)molecular adaptor activity (GO:0060090)morphogenesis of an epithelium (GO:0002009)myofibril (GO:0030016)negative regulation of cell migration (GO:0030336)outer dense plaque of desmosome (GO:0090636)perinuclear region of cytoplasm (GO:0048471)perinuclear region of cytoplasm (GO:0048471)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane (GO:0005886)platelet aggregation (GO:0070527)podosome (GO:0002102)protein binding (GO:0005515)protein localization to cell surface (GO:0034394)protein-containing complex (GO:0032991)regulation of establishment of endothelial barrier (GO:1903140)regulation of focal adhesion assembly (GO:0051893)regulation of focal adhesion assembly (GO:0051893)regulation of protein localization to adherens junction (GO:1904702)sarcolemma (GO:0042383)sarcolemma (GO:0042383)secretory granule lumen (GO:0034774)specific granule lumen (GO:0035580)structural molecule activity (GO:0005198)terminal web (GO:1990357)ubiquitin protein ligase binding (GO:0031625)zonula adherens (GO:0005915)

Expression (TPM)

TFs regulating VCL 0 TFs

Transcription factors with Perturb-seq knockdown data for VCL. 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 = VCL 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

Rows:

Elements linked to VCL

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of VCL, 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.

Element	Dist. to TSS	Link type	TFs
chr10:73,730,165–73,730,854	267.6 kb	Distal (>10kb) Multiome	823
chr10:73,741,689–73,742,673	256.0 kb	Distal (>10kb) Multiome	190
chr10:73,743,801–73,744,894	253.8 kb	Distal (>10kb) Multiome	962
chr10:73,771,782–73,773,237	225.3 kb	Distal (>10kb) Multiome	918
chr10:73,781,688–73,782,352	216.1 kb	Distal (>10kb) Multiome	721
chr10:73,785,180–73,785,869	212.6 kb	Distal (>10kb) Multiome	745
chr10:73,810,828–73,812,285	186.2 kb	Distal (>10kb) Multiome	876
chr10:73,817,045–73,817,772	180.8 kb	Distal (>10kb) Multiome	123
chr10:73,823,062–73,824,101	174.6 kb	Distal (>10kb) Multiome	130
chr10:73,873,847–73,875,246	123.5 kb	Distal (>10kb) Multiome	654
chr10:73,906,669–73,907,201	91.2 kb	Distal (>10kb) Multiome	417
chr10:73,910,388–73,911,812	87.0 kb	Distal (>10kb) Multiome	486
chr10:73,965,730–73,966,725	31.9 kb	Distal (>10kb) Multiome	552
chr10:73,994,650–73,995,392	3.0 kb	Proximal (<10kb) Multiome	69
chr10:73,997,294–73,999,626	197 bp	At TSS Multiome	964
chr10:74,150,306–74,151,881	153.1 kb	Distal (>10kb) Multiome	926
chr10:74,176,195–74,177,295	178.5 kb	Distal (>10kb) Multiome	1072

Genome Browser

Genomic view of the VCL 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.