VPS4A

vacuolar protein sorting 4 homolog A | FLJ22197, SKD1, SKD1A, SKD2, VPS4, VPS4-1

The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. The mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be really an yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 16; the gene for the other resides on chromosome 18. [provided by RefSeq, Jul 2008]

Member of: DE-6 DE-6.2

Biological processes 100 terms

ATP binding (GO:0005524)ATP binding (GO:0005524)ATP hydrolysis activity (GO:0016887)ATP hydrolysis activity (GO:0016887)ATP hydrolysis activity (GO:0016887)ATP hydrolysis activity (GO:0016887)ATP-dependent protein disaggregase activity (GO:0140545)ATP-dependent protein disaggregase activity (GO:0140545)ESCRT III complex disassembly (GO:1904903)ESCRT complex disassembly (GO:1904896)Flemming body (GO:0090543)Flemming body (GO:0090543)actomyosin contractile ring contraction (GO:0000916)autophagosome maturation (GO:0097352)autophagy (GO:0006914)cell division (GO:0051301)centrosome (GO:0005813)centrosome (GO:0005813)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoplasm (GO:0005737)cytoskeleton-dependent cytokinesis (GO:0061640)cytosol (GO:0005829)cytosol (GO:0005829)early endosome (GO:0005769)endosomal transport (GO:0016197)endosomal transport (GO:0016197)endosomal vesicle fusion (GO:0034058)endosome (GO:0005768)endosome (GO:0005768)endosome membrane (GO:0010008)extracellular exosome (GO:0070062)intracellular cholesterol transport (GO:0032367)late endosomal microautophagy (GO:0061738)late endosomal microautophagy (GO:0061738)late endosome (GO:0005770)late endosome membrane (GO:0031902)late endosome to lysosome transport via multivesicular body sorting pathway (GO:0061764)lysosomal transport (GO:0007041)lysosome (GO:0005764)macroautophagy (GO:0016236)membrane fission (GO:0090148)membrane fission (GO:0090148)midbody (GO:0030496)midbody (GO:0030496)midbody (GO:0030496)midbody (GO:0030496)midbody abscission (GO:0061952)midbody abscission (GO:0061952)midbody abscission (GO:0061952)mitotic cytokinesis checkpoint signaling (GO:0044878)mitotic metaphase chromosome alignment (GO:0007080)mitotic metaphase chromosome alignment (GO:0007080)mitotic nuclear membrane reassembly (GO:0007084)multivesicular body assembly (GO:0036258)multivesicular body assembly (GO:0036258)multivesicular body assembly (GO:0036258)multivesicular body sorting pathway (GO:0071985)negative regulation of cytokinesis (GO:0032466)nuclear envelope organization (GO:0006998)nuclear membrane reassembly (GO:0031468)nuclear membrane reassembly (GO:0031468)nucleus (GO:0005634)nucleus organization (GO:0006997)nucleus organization (GO:0006997)nucleus organization (GO:0006997)perinuclear region of cytoplasm (GO:0048471)perinuclear region of cytoplasm (GO:0048471)plasma membrane (GO:0005886)plasma membrane (GO:0005886)plasma membrane repair (GO:0001778)positive regulation of exosomal secretion (GO:1903543)positive regulation of exosomal secretion (GO:1903543)positive regulation of viral budding via host ESCRT complex (GO:1903774)protein binding (GO:0005515)protein depolymerization (GO:0051261)protein targeting to lysosome (GO:0006622)protein-containing complex binding (GO:0044877)regulation of G2/M transition of mitotic cell cycle (GO:0010389)regulation of protein localization (GO:0032880)regulation of protein localization to plasma membrane (GO:1903076)spindle (GO:0005819)spindle pole (GO:0000922)spindle pole (GO:0000922)ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043162)ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway (GO:0090611)ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway (GO:0090611)ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway (GO:0090611)vacuolar membrane (GO:0005774)vacuole organization (GO:0007033)vesicle budding from membrane (GO:0006900)vesicle uncoating (GO:0072319)vesicle-mediated transport (GO:0016192)viral budding from plasma membrane (GO:0046761)viral budding from plasma membrane (GO:0046761)viral budding via host ESCRT complex (GO:0039702)viral budding via host ESCRT complex (GO:0039702)viral release from host cell (GO:0019076)

Expression (TPM)

TFs regulating VPS4A 0 TFs

Transcription factors with Perturb-seq knockdown data for VPS4A. 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 = VPS4A 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 VPS4A

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of VPS4A, 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
chr16:68,843,238–68,844,359	467.6 kb	Distal (>10kb) Multiome HiCAR	918
chr16:69,071,809–69,072,879	239.0 kb	Distal (>10kb) Multiome	386
chr16:69,105,371–69,107,181	205.1 kb	Distal (>10kb) Multiome	631
chr16:69,131,353–69,133,059	178.9 kb	Distal (>10kb) Multiome	961
chr16:69,170,078–69,170,680	141.0 kb	Distal (>10kb) Multiome	43
chr16:69,186,569–69,187,845	124.2 kb	Distal (>10kb) Multiome	878
chr16:69,310,637–69,312,153	89 bp	At TSS Multiome	963
chr16:69,329,919–69,331,310	19.3 kb	Distal (>10kb) Multiome	977
chr16:69,339,182–69,340,174	28.3 kb	Distal (>10kb) Multiome	1014
chr16:69,385,555–69,386,170	74.6 kb	Distal (>10kb) Multiome	857
chr16:69,424,128–69,425,019	113.2 kb	Distal (>10kb) Multiome	907
chr16:69,529,449–69,529,941	218.4 kb	Distal (>10kb) Multiome	450
chr16:69,565,464–69,566,984	254.5 kb	Distal (>10kb) Multiome	1044

Genome Browser

Genomic view of the VPS4A 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.