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

Gene ID: 51160, updated on 3-Apr-2024

Summary

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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
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Genomic context

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See VPS28 in Genome Data Viewer
Location:
8q24.3
Exon count:
11
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 8 NC_000008.11 (144423617..144428548, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 8 NC_060932.1 (145593428..145598361, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 8 NC_000008.10 (145649000..145653931, complement)

Chromosome 8 - NC_000008.11Genomic Context describing neighboring genes Neighboring gene cleavage and polyadenylation specific factor 1 Neighboring gene microRNA 6849 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28097 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19681 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19682 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 28098 Neighboring gene ReSE screen-validated silencer GRCh37_chr8:145638844-145639041 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145639267-145640084 Neighboring gene uncharacterized LOC124902041 Neighboring gene solute carrier family 39 member 4 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145647393-145648164 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145648165-145648934 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr8:145651263-145652026 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19684 Neighboring gene tonsoku like, DNA repair protein Neighboring gene TONSL antisense RNA 1 Neighboring gene microRNA 6893 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145668715-145669223 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19685 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 19686 Neighboring gene TMEM276-ZFTRAF1 readthrough Neighboring gene zinc finger TRAF-type containing 1 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr8:145687825-145688502 Neighboring gene microRNA 10400

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Protein sorting into multivesicular endosomes. Raiborg C, et al. Curr Opin Cell Biol, 2003 Aug. PMID 12892785
  2. Equine infectious anemia virus utilizes host vesicular protein sorting machinery during particle release. Tanzi GO, et al. J Virol, 2003 Aug. PMID 12857913, Free PMC Article
  3. CIIA negatively regulates the Ras-Erk1/2 signaling pathway through inhibiting the Ras-specific GEF activity of SOS1. Hwang HS, et al. J Cell Sci, 2014 Apr 15. PMID 24522193
  4. Solution structure of the ESCRT-I complex by small-angle X-ray scattering, EPR, and FRET spectroscopy. Boura E, et al. Proc Natl Acad Sci U S A, 2011 Jun 7. PMID 21596998, Free PMC Article
  5. YPXL/I is a protein interaction motif recognized by aspergillus PalA and its human homologue, AIP1/Alix. Vincent O, et al. Mol Cell Biol, 2003 Mar. PMID 12588984, Free PMC Article

See all (91) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
Submit: New GeneRIF Correction

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

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

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

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • MGC60323

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 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

  1. NG_029456.2 RefSeqGene

    Range
    4997..9928
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. 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_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000008.11 Reference GRCh38.p14 Primary Assembly

    Range
    144423617..144428548 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. 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

  2. XM_047421845.1 → XP_047277801.1  vacuolar protein sorting-associated protein 28 homolog isoform X2

  3. XM_047421846.1 → XP_047277802.1  vacuolar protein sorting-associated protein 28 homolog isoform X2

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_018654716.1 Reference GRCh38.p14 PATCHES

    Range
    154219..159150 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0S2Z5H5

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060932.1 Alternate T2T-CHM13v2.0

    Range
    145593428..145598361 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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

    UniProtKB/TrEMBL
    A0A0S2Z5H5

  2. XM_054360614.1 → XP_054216589.1  vacuolar protein sorting-associated protein 28 homolog isoform X2

Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9UK41.1 GenPept UniProtKB/Swiss-Prot:Q9UK41

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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