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    VPS36 vacuolar protein sorting 36 homolog [ Homo sapiens (human) ]

    Gene ID: 51028, updated on 27-Nov-2024

    Summary

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    Official Symbol
    VPS36provided by HGNC
    Official Full Name
    vacuolar protein sorting 36 homologprovided by HGNC
    Primary source
    HGNC:HGNC:20312
    See related
    Ensembl:ENSG00000136100 MIM:610903; AllianceGenome:HGNC:20312
    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
    EAP45; C13orf9; CGI-145
    Summary
    This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A similar protein complex in rat is associated with RNA polymerase elongation factor II. [provided by RefSeq, Aug 2013]
    Expression
    Ubiquitous expression in skin (RPKM 25.0), thyroid (RPKM 15.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See VPS36 in Genome Data Viewer
    Location:
    13q14.3
    Exon count:
    15
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 13 NC_000013.11 (52412606..52450634, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 13 NC_060937.1 (51627427..51665457, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 13 NC_000013.10 (52986741..53024769, complement)

    Chromosome 13 - NC_000013.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370207 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr13:52922389-52923588 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52951563-52952064 Neighboring gene H3K27ac hESC enhancer GRCh37_chr13:52952065-52952564 Neighboring gene thrombospondin type 1 domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5384 Neighboring gene RNY4 pseudogene 24 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr13:53024355-53024935 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5386 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 7791 Neighboring gene CKAP2 divergent transcript Neighboring gene cytoskeleton associated protein 2

    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. Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain. Alam SL, et al. Nat Struct Mol Biol, 2006 Nov. PMID 17057716
    2. Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein. Kaewborisuth C, et al. Viruses, 2019 Apr 24. PMID 31022991, Free PMC Article
    3. RAB27A, RAB27B and VPS36 are downregulated in advanced prostate cancer and show functional relevance in prostate cancer cells. Worst TS, et al. Int J Oncol, 2017 Mar. PMID 28197629
    4. Structural insight into the ESCRT-I/-II link and its role in MVB trafficking. Gill DJ, et al. EMBO J, 2007 Jan 24. PMID 17215868, Free PMC Article
    5. Integrated structural model and membrane targeting mechanism of the human ESCRT-II complex. Im YJ, et al. Dev Cell, 2008 Jun. PMID 18539118, Free PMC Article

    See all (52) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. As a result of VPS36-ORF3 interaction, Porcine Epidemic Diarrhea Virus replication was substantially suppressed in cells overexpressing VPS36.
      Title: Porcine Epidemic Diarrhea Virus (PEDV) ORF3 Interactome Reveals Inhibition of Virus Replication by Cellular VPS36 Protein.
    2. RAB27A, RAB27B and VPS36 are frequently underexpressed in advanced prostate cancer and are inversely correlated with prostate cancer outcome. There seems to be a close relationship in the expression of RAB27A, RAB27B and VPS36, with RAB27A and RAB27B being dependent on VPS36.
      Title: RAB27A, RAB27B and VPS36 are downregulated in advanced prostate cancer and show functional relevance in prostate cancer cells.
    3. mammalian ESCRTII is made up of hVps25p, hVps22p, and hVps36p and may be redundant, cargo-specific, or not required for protein sorting at the multivesicular body
      Title: Degradation of endocytosed epidermal growth factor and virally ubiquitinated major histocompatibility complex class I is independent of mammalian ESCRTII.
    4. Crystallographic and biochemical analyses reveal that the GLUE domain of the human ESCRT-II EAP45 (also called VPS36) subunit is a split pleckstrin-homology domain that binds ubiquitin along one edge of the beta-sandwich.
      Title: Structural basis for ubiquitin recognition by the human ESCRT-II EAP45 GLUE domain.
    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

    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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    Replication interactions

    Interaction Pubs
    shRNA knockdown of VPS36 (ESCRT-II component) decreases HIV-1 CA-p24 supernatant levels when using wild type (HIV-1 LAI) and VSV-pseudotyped virus; HIV replication is enhanced by VPS36 PubMed
    CRISPR/Cas9 knockout of VPS36 (EAP45) reduces intracellular CA (p24) in, and reduces virion-associated CA (p24) release from, pHIV (BH10)-transfected HAP1 cells (Haplogen GmbH, Vienna, Austria); VPS36 enhances HIV-1 replication PubMed

    Protein interactions

    Protein Gene Interaction Pubs
    capsid gag Knockdown of VPS36 (ESCRT-II component) decreases HIV-1 CA-p24 secretion when using wild type (HIV-1 LAI) and VSV-pseudotyped virus PubMed
    gag Knockout of VPS36 (EAP45) reduces virion-associated CA (p24) release from HAP1 cells PubMed
    gag Knockout of VPS36 (EAP45) reduces intracellular CA (p24) in HAP1 cells PubMed
    gag The EAP45 mutant, IERK159-162AAAA, (that substantially reduces ESCRTII-ESCRTI interaction in vitro), impairs the production of extracellular CA-p24 PubMed
    gag The EAP45 mutant, IERK159-162AAAA, (substantially reduces ESCRTII-ESCRTI interaction in vitro), impairs the production of intracellular CA-p24 PubMed
    gag Overexpression of GLUE (GRAM-like ubiquitin-binding in EAP45) domain in isolation (amino acids 1-139, not sufficient to interact with ESCRT-I) decreases extracellular CA-p24 levels PubMed
    gag Overexpression of GLUE (GRAM-like ubiquitin-binding in EAP45) domain in isolation (amino acids 1-139, not sufficient to interact with ESCRT-I) impairs the production of intracellular CA-p24 PubMed
    gag Knockdown of VPS36 (ESCRT-II component) impairs HIV-1 CA-p24 production when using wild type (HIV-1 LAI) and VSV-pseudotyped virus 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

    Potential readthrough

    Included gene: THSD1

    Homology

    Clone Names

    • DKFZp781E0871

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables phosphatidylinositol-3-phosphate binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables ubiquitin binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables ubiquitin binding IMP
    Inferred from Mutant Phenotype
    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 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 
    Component Evidence Code Pubs
    part_of ESCRT II complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of ESCRT II complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of ESCRT II complex IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    part_of ESCRT II complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in extracellular exosome HDA PubMed 
    is_active_in late endosome membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in late endosome membrane IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in lysosome IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nucleus IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    vacuolar protein-sorting-associated protein 36
    Names
    ELL-associated protein of 45 kDa
    ESCRT-II complex subunit VPS36

    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.

    mRNA and Protein(s)

    1. NM_001282168.2 → NP_001269097.1  vacuolar protein-sorting-associated protein 36 isoform 2

      See identical proteins and their annotated locations for NP_001269097.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' terminal exon compared to variant 1. This results in a shorter protein (isoform 2) compared to isoform 1.
      Source sequence(s)
      AI352102, AL359513, BX647847, CB959894, DA461148
      Conserved Domains (2) summary
      cd13226
      Location:1 → 119
      PH-GRAM-like_Eap45; Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Eap45
      pfam04157
      Location:146 → 360
      EAP30; EAP30/Vps36 family

    2. NM_001282169.2 → NP_001269098.1  vacuolar protein-sorting-associated protein 36 isoform 3

      See identical proteins and their annotated locations for NP_001269098.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' terminal exon, lacks a portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (3) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AI221133, AI352102, AL359513
      Consensus CDS
      CCDS73577.1
      UniProtKB/Swiss-Prot
      Q86VN1
      Related
      ENSP00000484968.1, ENST00000611132.4
      Conserved Domains (2) summary
      pfam04157
      Location:96 → 311
      EAP30; EAP30/Vps36 family
      cl17171
      Location:1 → 70
      PH-like; Pleckstrin homology-like domain

    3. NM_016075.4 → NP_057159.2  vacuolar protein-sorting-associated protein 36 isoform 1

      See identical proteins and their annotated locations for NP_057159.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AI352102, AK289740, BC037279, DA461148
      Consensus CDS
      CCDS9434.1
      UniProtKB/Swiss-Prot
      A8K125, Q3ZCV7, Q5H9S1, Q5VXB6, Q86VN1, Q9H8Z5, Q9Y3E3
      Related
      ENSP00000367299.3, ENST00000378060.9
      Conserved Domains (2) summary
      cd13226
      Location:1 → 128
      PH-GRAM-like_Eap45; Pleckstrin homology-like domain or GLUE (GRAM-like ubiquitin-binding in Eap45) domain of Eap45
      pfam04157
      Location:154 → 369
      EAP30; EAP30/Vps36 family

    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

    1. NC_000013.11 Reference GRCh38.p14 Primary Assembly

      Range
      52412606..52450634 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060937.1 Alternate T2T-CHM13v2.0

      Range
      51627427..51665457 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86VN1.1 GenPept UniProtKB/Swiss-Prot:Q86VN1

    Gene LinkOut

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

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