VPS11
VPS11 core subunit of CORVET and HOPS complexes | PEP5, RNF108

Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]

Biological processes 45 terms
HOPS complex (GO:0030897)HOPS complex (GO:0030897)autophagosome (GO:0005776)autophagosome-lysosome fusion (GO:0061909)clathrin-coated vesicle (GO:0030136)cytoplasmic vesicle (GO:0031410)early endosome (GO:0005769)early endosome (GO:0005769)endocytic vesicle (GO:0030139)endosomal vesicle fusion (GO:0034058)endosomal vesicle fusion (GO:0034058)endosome (GO:0005768)endosome (GO:0005768)endosome (GO:0005768)endosome membrane (GO:0010008)endosome organization (GO:0007032)endosome to lysosome transport (GO:0008333)intracellular protein transport (GO:0006886)late endosome (GO:0005770)late endosome (GO:0005770)late endosome membrane (GO:0031902)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosomal membrane (GO:0005765)lysosome (GO:0005764)lysosome (GO:0005764)molecular adaptor activity (GO:0060090)negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)organelle fusion (GO:0048284)positive regulation of early endosome to late endosome transport (GO:2000643)positive regulation of protein catabolic process (GO:0045732)positive regulation of protein localization to mitochondrion (GO:1903749)protein binding (GO:0005515)protein domain specific binding (GO:0019904)protein ubiquitination (GO:0016567)protein-macromolecule adaptor activity (GO:0030674)regulation of SNARE complex assembly (GO:0035542)regulation of organelle assembly (GO:1902115)regulation of protein stability (GO:0031647)syntaxin binding (GO:0019905)ubiquitin protein ligase activity (GO:0061630)vacuole organization (GO:0007033)vesicle docking involved in exocytosis (GO:0006904)vesicle tethering complex (GO:0099023)vesicle-mediated transport (GO:0016192)
Expression (TPM)
VPS11 — as a Regulated Gene

TFs regulating VPS11 0 TFs

Transcription factors with Perturb-seq knockdown data for VPS11. 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 = VPS11 upregulated upon KD; negative = downregulated). The Outlier column indicates whether this gene is in the top or bottom 5% of all TF knockdown effects.

Data: Effect:
TF Mean coef Binding Outlier TF→Gene link

Elements linked to VPS11

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of VPS11, 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
chr11:118,789,603–118,790,362 278.0 kb Distal (>10kb) Multiome 293
chr11:118,790,448–118,793,117 274.9 kb Distal (>10kb) Multiome 958
chr11:118,907,074–118,907,685 160.5 kb Distal (>10kb) Multiome 491
chr11:118,909,181–118,909,816 158.4 kb Distal (>10kb) Multiome 326
chr11:118,909,976–118,911,609 157.2 kb Distal (>10kb) Multiome 652
chr11:118,911,717–118,912,963 155.5 kb Distal (>10kb) Multiome 689
chr11:118,916,429–118,917,335 150.9 kb Distal (>10kb) Multiome 355
chr11:118,917,640–118,918,851 149.4 kb Distal (>10kb) Multiome 522
chr11:118,925,703–118,926,356 141.8 kb Distal (>10kb) Multiome 595
chr11:118,927,947–118,930,852 138.4 kb Distal (>10kb) Multiome 892
chr11:118,997,538–118,998,797 69.7 kb Distal (>10kb) Multiome 798
chr11:119,018,081–119,019,265 49.3 kb Distal (>10kb) Multiome 897
chr11:119,029,885–119,031,330 36.9 kb Distal (>10kb) Multiome 876
chr11:119,056,436–119,057,778 10.5 kb Distal (>10kb) Multiome 815
chr11:119,067,446–119,068,100 76 bp At TSS Multiome 762
chr11:119,084,563–119,085,756 17.2 kb Distal (>10kb) Multiome 846
chr11:119,093,969–119,096,070 27.7 kb Distal (>10kb) Multiome 1046
chr11:119,101,351–119,102,791 34.3 kb Distal (>10kb) Multiome 871
chr11:119,106,906–119,107,993 39.5 kb Distal (>10kb) Multiome 650
chr11:119,120,857–119,122,037 53.6 kb Distal (>10kb) Multiome 787
chr11:119,144,795–119,145,355 77.3 kb Distal (>10kb) Multiome 230
chr11:119,148,816–119,149,933 81.8 kb Distal (>10kb) Multiome 262
chr11:119,168,601–119,169,645 101.1 kb Distal (>10kb) Multiome 794
chr11:119,205,241–119,207,150 138.3 kb Distal (>10kb) Multiome 695
chr11:119,315,017–119,315,819 247.5 kb Distal (>10kb) Multiome 270
chr11:119,316,693–119,317,760 249.4 kb Distal (>10kb) Multiome 463
chr11:119,320,617–119,321,906 253.9 kb Distal (>10kb) Multiome 516
chr11:119,334,140–119,334,815 266.6 kb Distal (>10kb) Multiome 577
chr11:119,337,716–119,338,797 270.5 kb Distal (>10kb) Multiome 412
chr11:119,339,587–119,340,902 272.3 kb Distal (>10kb) Multiome 477
chr11:119,356,332–119,357,013 288.9 kb Distal (>10kb) Multiome 366
chr11:119,361,041–119,361,699 293.5 kb Distal (>10kb) Multiome 431
chr11:119,363,939–119,364,561 296.4 kb Distal (>10kb) Multiome 255

Genome Browser

Genomic view of the VPS11 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.

chr11:118,779,603 – 119,374,561
Proximal 1 kb Distal 10 kb Multiome HiCAR ATAC-seq RNA-seq
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