VPS28 VPS28 subunit of ESCRT-I [Homo sapiens (human)] - Gene

Summary

Official Symbol: VPS28provided by HGNC
Official Full Name: VPS28 subunit of ESCRT-Iprovided by HGNC
Primary source: HGNC:HGNC:18178
See related: Ensembl:ENSG00000160948 MIM:611952; AllianceGenome:HGNC:18178
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: CIIA
Summary: 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]
Expression: Ubiquitous expression in ovary (RPKM 46.0), duodenum (RPKM 44.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 8q24.3

Exon count:: 11

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	8	NC_000008.11 (144423617..144428548, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	8	NC_060932.1 (145593428..145598361, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	8	NC_000008.10 (145649000..145653931, complement)

Chromosome 8 - NC_000008.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

VPS28, an ESCRT-I protein, interacts with Gbetagamma and Eg5-TPX2. VPS28 organizes Aster Microtubules via Gbetagamma. VPS28 recruits Eg5 and TPX2 to regulate mitotic spindle bipolarity.
Title: VPS28, an ESCRT-I protein, regulates mitotic spindle organization via Gβγ, EG5 and TPX2.
CIIA attenuates neurotoxicity caused by OGD/R through inhibiting ASK1-dependent signaling events.
Title: CIIA negatively regulates neuronal cell death induced by oxygen-glucose deprivation and reoxygenation.
USP8, and the endosomal sorting protein, VPS28, are the negative regulators of NOD2-induced IL-8 secretion.
Title: A genome-wide small interfering RNA (siRNA) screen reveals nuclear factor-κB (NF-κB)-independent regulators of NOD2-induced interleukin-8 (IL-8) secretion.
CIIA functions as a negative modulator of the SOS1-Ras signaling events initiated by peptide growth factors including EGF.
Title: CIIA negatively regulates the Ras-Erk1/2 signaling pathway through inhibiting the Ras-specific GEF activity of SOS1.
Data show that gamma2-adaptin in MVB sorting specifically interacts with the ESCRT subunits Vps28 and CHMP2A.
Title: γ2-Adaptin is functioning in the late endosomal sorting pathway and interacts with ESCRT-I and -III subunits.
Overall, we see no role for the ESCRT pathway in influenza virus budding and the significance of the M1-VPS28 interaction remains to be determined.
Title: Budding of filamentous and non-filamentous influenza A virus occurs via a VPS4 and VPS28-independent pathway.
EIAV Gag interacts with a cellular component of the VPS machinery, VPS28, to accomplish efficient particle release
Title: Equine infectious anemia virus utilizes host vesicular protein sorting machinery during particle release.

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Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Common genetic variants associated with cognitive performance identified using the proxy-phenotype method. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Pr55(Gag)	gag	Tsg 101, VPS 28, and VPS 37B form the human endosomal sorting complex required for transport (ESCRT-I), which is required for HIV-1 Gag budding and virus infectivity	PubMed
p6	gag	ESCRT-I complexes contain three common subunits (TSG101, VPS28, and VPS37), and a fourth subunit MVB12. Recombinant ESCRT-I complexes bind HIV-1 p6	PubMed

Go to the HIV-1, Human Interaction Database

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH16000 (e-PCR)
- UniSTS:88627

D10S16 (e-PCR)
- UniSTS:155756

MARC_23623-23624:1027527533:1 (e-PCR)
- UniSTS:268725

A006J21 (e-PCR)
- UniSTS:57306

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-containing complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables ubiquitin binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in macroautophagy	TAS Traceable Author Statement more info	PubMed
involved_in membrane fission	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body assembly	NAS Non-traceable Author Statement more info	PubMed
involved_in multivesicular body assembly	TAS Traceable Author Statement more info	PubMed
involved_in negative regulation of protein ubiquitination	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of protein catabolic process	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of ubiquitin-dependent endocytosis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in protein transport to vacuole involved in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	NAS Non-traceable Author Statement more info	PubMed
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IC Inferred by Curator more info	PubMed
involved_in ubiquitin-dependent protein catabolic process via the multivesicular body sorting pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in viral budding via host ESCRT complex	TAS Traceable Author Statement more info	PubMed

Component	Evidence Code	Pubs
part_of ESCRT I complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ESCRT I complex	IDA Inferred from Direct Assay more info	PubMed
part_of ESCRT I complex	IPI Inferred from Physical Interaction more info	PubMed
part_of ESCRT I complex	ISS Inferred from Sequence or Structural Similarity more info
part_of ESCRT I complex	TAS Traceable Author Statement more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in early endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	IDA Inferred from Direct Assay more info	PubMed
located_in endosome membrane	NAS Non-traceable Author Statement more info	PubMed
located_in endosome membrane	TAS Traceable Author Statement more info
located_in extracellular exosome	HDA more info	PubMed
located_in late endosome membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: vacuolar protein sorting-associated protein 28 homolog

Names: ESCRT-I complex subunit VPS28; VPS28, ESCRT-I subunit; vacuolar protein sorting 28 homolog; vacuolar protein sorting 28-like protein; yeast class E protein Vps28p homolog

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_029456.2 RefSeqGene

Range

4997..9928

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_016208.4 → NP_057292.1 vacuolar protein sorting-associated protein 28 homolog isoform 1

See identical proteins and their annotated locations for NP_057292.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the shorter transcript and encodes the shorter isoform (1).

Source sequence(s)

AK026865, BC050438, BP380505, R72904

Consensus CDS

CCDS6425.1

UniProtKB/Swiss-Prot

Q86VK0, Q9UK41

UniProtKB/TrEMBL

E9PM90, Q548N1

Related

ENSP00000292510.3, ENST00000292510.6

Conserved Domains (1) summary

pfam03997
Location:39 → 219

VPS28; VPS28 protein
NM_183057.3 → NP_898880.1 vacuolar protein sorting-associated protein 28 homolog isoform 2

See identical proteins and their annotated locations for NP_898880.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate segment in ther 3' coding region, which results in a frameshift, compared to variant 1. The encoded isoform (2) is longer and has a distinct C-terminus, compared to isoform 1.

Source sequence(s)

BC050713, BP380505, R72904

Consensus CDS

CCDS34967.1

UniProtKB/Swiss-Prot

Q9UK41

Related

ENSP00000366565.2, ENST00000377348.6

Conserved Domains (1) summary

pfam03997
Location:39 → 187

VPS28; VPS28 protein

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000008.11 Reference GRCh38.p14 Primary Assembly

Range

144423617..144428548 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_005272324.4 → XP_005272381.1 vacuolar protein sorting-associated protein 28 homolog isoform X1

UniProtKB/TrEMBL

A0A0S2Z5H5, E9PM90

Related

ENSP00000431243.1, ENST00000533806.5

Conserved Domains (1) summary

pfam03997
Location:39 → 202

VPS28; VPS28 protein
XM_047421845.1 → XP_047277801.1 vacuolar protein sorting-associated protein 28 homolog isoform X2
XM_047421846.1 → XP_047277802.1 vacuolar protein sorting-associated protein 28 homolog isoform X2

Reference GRCh38.p14 PATCHES

Genomic

NW_018654716.1 Reference GRCh38.p14 PATCHES

Range

154219..159150 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054332201.1 → XP_054188176.1 vacuolar protein sorting-associated protein 28 homolog isoform X1

UniProtKB/TrEMBL

A0A0S2Z5H5, E9PM90

Alternate T2T-CHM13v2.0

Genomic

NC_060932.1 Alternate T2T-CHM13v2.0

Range

145593428..145598361 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054360613.1 → XP_054216588.1 vacuolar protein sorting-associated protein 28 homolog isoform X1

UniProtKB/TrEMBL

A0A0S2Z5H5, E9PM90
XM_054360614.1 → XP_054216589.1 vacuolar protein sorting-associated protein 28 homolog isoform X2