VPS28

VPS28 subunit of ESCRT-I | CIIA

This gene encodes a protein subunit of the ESCRT-I complex (endosomal complexes required for transport), which functions in the transport and sorting of proteins into subcellular vesicles. This complex can also be hijacked to facilitate the budding of enveloped viruses from the cell membrane. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2013]

Member of: DE-1 Developmental clusters: GC6

Biological processes 36 terms

ESCRT I complex (GO:0000813)ESCRT I complex (GO:0000813)ESCRT I complex (GO:0000813)ESCRT I complex (GO:0000813)cytoplasm (GO:0005737)cytosol (GO:0005829)cytosol (GO:0005829)cytosol (GO:0005829)early endosome (GO:0005769)endosome (GO:0005768)endosome membrane (GO:0010008)endosome membrane (GO:0010008)endosome membrane (GO:0010008)endosome transport via multivesicular body sorting pathway (GO:0032509)extracellular exosome (GO:0070062)late endosome membrane (GO:0031902)macroautophagy (GO:0016236)macroautophagy (GO:0016236)membrane fission (GO:0090148)multivesicular body assembly (GO:0036258)multivesicular body assembly (GO:0036258)multivesicular body assembly (GO:0036258)negative regulation of protein ubiquitination (GO:0031397)plasma membrane (GO:0005886)plasma membrane (GO:0005886)positive regulation of protein catabolic process (GO:0045732)positive regulation of ubiquitin-dependent endocytosis (GO:2000397)protein binding (GO:0005515)protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043328)protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway (GO:0043328)ubiquitin binding (GO:0043130)ubiquitin binding (GO:0043130)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)viral budding via host ESCRT complex (GO:0039702)viral budding via host ESCRT complex (GO:0039702)

Expression (TPM)

TFs regulating VPS28 0 TFs

Transcription factors with Perturb-seq knockdown data for VPS28. 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 = VPS28 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 VPS28

Open chromatin peaks (ATAC-seq) in the genomic neighbourhood of VPS28, 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
chr8:144,137,565–144,138,500	290.8 kb	Distal (>10kb) Multiome	817
chr8:144,146,820–144,149,073	280.6 kb	Distal (>10kb) Multiome	790
chr8:144,266,293–144,267,098	162.1 kb	Distal (>10kb) Multiome	162
chr8:144,290,981–144,292,410	137.1 kb	Distal (>10kb) Multiome	716
chr8:144,315,833–144,316,450	112.4 kb	Distal (>10kb) Multiome	396
chr8:144,325,768–144,327,719	101.7 kb	Distal (>10kb) Multiome	1016
chr8:144,331,281–144,333,847	96.6 kb	Distal (>10kb) Multiome	406
chr8:144,336,102–144,339,119	91.7 kb	Distal (>10kb) Multiome	922
chr8:144,353,907–144,355,227	74.0 kb	Distal (>10kb) Multiome HiCAR	280
chr8:144,358,142–144,359,070	70.0 kb	Distal (>10kb) Multiome HiCAR	719
chr8:144,369,349–144,369,916	58.9 kb	Distal (>10kb) Multiome HiCAR	204
chr8:144,372,497–144,372,883	55.8 kb	Distal (>10kb) Multiome HiCAR	160
chr8:144,372,993–144,375,084	54.6 kb	Distal (>10kb) Multiome HiCAR	903
chr8:144,408,968–144,410,189	19.1 kb	Distal (>10kb) Multiome	920
chr8:144,427,691–144,429,571	24 bp	At TSS Multiome	1000
chr8:144,443,691–144,445,047	15.8 kb	Distal (>10kb) Multiome	743
chr8:144,462,568–144,463,422	34.4 kb	Distal (>10kb) Multiome	548
chr8:144,463,885–144,468,178	37.2 kb	Distal (>10kb) Multiome	910
chr8:144,471,960–144,474,391	44.0 kb	Distal (>10kb) Multiome	482
chr8:144,474,517–144,476,543	47.3 kb	Distal (>10kb) Multiome	321
chr8:144,477,277–144,478,749	49.4 kb	Distal (>10kb) Multiome	679
chr8:144,478,851–144,479,509	50.7 kb	Distal (>10kb) Multiome	392
chr8:144,483,979–144,484,843	55.8 kb	Distal (>10kb) Multiome	125
chr8:144,495,748–144,496,431	67.5 kb	Distal (>10kb) Multiome	131
chr8:144,500,182–144,501,505	72.4 kb	Distal (>10kb) Multiome	484
chr8:144,507,995–144,510,268	80.3 kb	Distal (>10kb) Multiome	1067
chr8:144,517,168–144,518,442	89.3 kb	Distal (>10kb) Multiome	637
chr8:144,521,935–144,523,450	94.0 kb	Distal (>10kb) Multiome	663
chr8:144,524,105–144,525,099	96.1 kb	Distal (>10kb) Multiome	264
chr8:144,526,399–144,529,305	98.5 kb	Distal (>10kb) Multiome	934
chr8:144,529,455–144,530,630	101.6 kb	Distal (>10kb) Multiome	284
chr8:144,580,290–144,581,657	152.2 kb	Distal (>10kb) Multiome	271
chr8:144,672,507–144,672,989	244.3 kb	Distal (>10kb) Multiome	150
chr8:144,684,108–144,686,340	255.8 kb	Distal (>10kb) Multiome	862

Genome Browser

Genomic view of the VPS28 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.