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    CHMP3 charged multivesicular body protein 3 [ Homo sapiens (human) ]

    Gene ID: 51652, updated on 17-Jun-2019

    Summary

    Official Symbol
    CHMP3provided by HGNC
    Official Full Name
    charged multivesicular body protein 3provided by HGNC
    Primary source
    HGNC:HGNC:29865
    See related
    Ensembl:ENSG00000115561 MIM:610052
    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
    NEDF; VPS24; CGI-149
    Summary
    This gene encodes a protein that sorts transmembrane proteins into lysosomes/vacuoles via the multivesicular body (MVB) pathway. This protein, along with other soluble coiled-coil containing proteins, forms part of the ESCRT-III protein complex that binds to the endosomal membrane and recruits additional cofactors for protein sorting into the MVB. This protein may also co-immunoprecipitate with a member of the IFG-binding protein superfamily. Alternative splicing results in multiple transcript variants. Read-through transcription also exists between this gene and the upstream ring finger protein 103 (RNF103) gene. [provided by RefSeq, Nov 2010]
    Expression
    Ubiquitous expression in esophagus (RPKM 41.6), thyroid (RPKM 40.0) and 25 other tissues See more
    Orthologs

    Genomic context

    See CHMP3 in Genome Data Viewer
    Location:
    2p11.2
    Exon count:
    6
    Annotation release Status Assembly Chr Location
    109.20190607 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (86503430..86563497, complement)
    105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (86730553..86790620, complement)

    Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 10968 Neighboring gene receptor accessory protein 1 Neighboring gene lysine demethylase 3A Neighboring gene RNF103-CHMP3 readthrough Neighboring gene RNA, U6 small nuclear 640, pseudogene Neighboring gene uncharacterized LOC105374845 Neighboring gene Sharpr-MPRA regulatory region 1991 Neighboring gene ring finger protein 103 Neighboring gene required for meiotic nuclear division 5 homolog A

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Envelope surface glycoprotein gp120 env Downregulation of guanine nucleotide-releasing protein, CD151/PETA-3, neuronatin, neuroendocrine differentiation factor, mitochondria 16s rRNA, and signal recognition particle is observed in HIV-1 infected and HIV-1 gp120-treated astrocytes PubMed
    Pr55(Gag) gag Recruitment of CHMP2A and CHMP3 by CHMP4B to HIV-1 Gag puncta is observed in in-vitro membrane model PubMed
    gag Replacing the NC-p1-p6 region of HIV-1 Gag with the leucine zipper domain of yeast GCN4 overcomes inhibition of HIV-1 particle budding by dominant-negative ESCRT proteins such as CHMP3 and Vps4A PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from BioSystems

    • Budding and maturation of HIV virion, organism-specific biosystem (from REACTOME)
      Budding and maturation of HIV virion, organism-specific biosystemWith the virus components precariously assembled on the inner leaflet of the plasma membrane, the host cell machinery is required for viral budding. The virus takes advantage of the host ESCRT pathwa...
    • Cellular responses to stress, organism-specific biosystem (from REACTOME)
      Cellular responses to stress, organism-specific biosystemCells are subject to external molecular and physical stresses such as foreign molecules that perturb metabolic or signaling processes, and changes in temperature or pH. The ability of cells and tissu...
    • Disease, organism-specific biosystem (from REACTOME)
      Disease, organism-specific biosystemBiological processes are captured in Reactome by identifying the molecules (DNA, RNA, protein, small molecules) involved in them and describing the details of their interactions. From this molecular ...
    • ESCRT-III complex, organism-specific biosystem (from KEGG)
      ESCRT-III complex, organism-specific biosystemStructural complex; Genetic information processing; Protein processing
    • ESCRT-III complex, conserved biosystem (from KEGG)
      ESCRT-III complex, conserved biosystemStructural complex; Genetic information processing; Protein processing
    • Endocytosis, organism-specific biosystem (from KEGG)
      Endocytosis, organism-specific biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
    • Endocytosis, conserved biosystem (from KEGG)
      Endocytosis, conserved biosystemEndocytosis is a mechanism for cells to remove ligands, nutrients, and plasma membrane (PM) proteins, and lipids from the cell surface, bringing them into the cell interior. Transmembrane proteins en...
    • Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystem (from REACTOME)
      Endosomal Sorting Complex Required For Transport (ESCRT), organism-specific biosystemMany plasma membrane proteins are in a constant flux throughout the internal trafficking pathways of the cell. Some receptors are continuously internalized into recycling endosomes and returned to th...
    • HIV Infection, organism-specific biosystem (from REACTOME)
      HIV Infection, organism-specific biosystemThe global pandemic of Human Immunodeficiency Virus (HIV) infection has resulted in tens of millions of people infected by the virus and millions more affected. UNAIDS estimates around 40 million ...
    • HIV Life Cycle, organism-specific biosystem (from REACTOME)
      HIV Life Cycle, organism-specific biosystemThe life cycle of HIV-1 is divided into early and late phases, shown schematically in the figure. In the early phase, an HIV-1 virion binds to receptors and co-receptors on the human host cell surfac...
    • Infectious disease, organism-specific biosystem (from REACTOME)
      Infectious disease, organism-specific biosystem
      Infectious disease
    • Internalization of ErbB1, organism-specific biosystem (from Pathway Interaction Database)
      Internalization of ErbB1, organism-specific biosystem
      Internalization of ErbB1
    • Late Phase of HIV Life Cycle, organism-specific biosystem (from REACTOME)
      Late Phase of HIV Life Cycle, organism-specific biosystemThe late phase of the HIV-1 life cycle includes the regulated expression of the HIV gene products and the assembly of viral particles. The assembly of viral particles will be covered in a later relea...
    • Macroautophagy, organism-specific biosystem (from REACTOME)
      Macroautophagy, organism-specific biosystemMacroautophagy (hereafter referred to as autophagy) acts as a buffer against starvation by liberating building materials and energy sources from cellular components. It has additional roles in embryo...
    • Membrane Trafficking, organism-specific biosystem (from REACTOME)
      Membrane Trafficking, organism-specific biosystemThe secretory membrane system allows a cell to regulate delivery of newly synthesized proteins, carbohydrates, and lipids to the cell surface, a necessity for growth and homeostasis. The system is ma...
    • Vesicle-mediated transport, organism-specific biosystem (from REACTOME)
      Vesicle-mediated transport, organism-specific biosystemThe transit of proteins and other cargo through the cell requires a cellular transport process in which transported substances are moved in membrane-bounded vesicles. Transported substances are enclo...

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Readthrough RNF103-CHMP3

    Readthrough gene: RNF103-CHMP3, Included gene: RNF103

    Homology

    Clone Names

    • FLJ38114

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    phosphatidylcholine binding IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    protein homodimerization activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    ubiquitin-specific protease binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    Process Evidence Code Pubs
    apoptotic process IEA
    Inferred from Electronic Annotation
    more info
     
    autophagosome maturation TAS
    Traceable Author Statement
    more info
    PubMed 
    endosomal transport TAS
    Traceable Author Statement
    more info
     
    endosome transport via multivesicular body sorting pathway IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    late endosome to vacuole transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    macroautophagy TAS
    Traceable Author Statement
    more info
    PubMed 
    midbody abscission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT mitotic metaphase plate congression IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    multivesicular body assembly TAS
    Traceable Author Statement
    more info
    PubMed 
    multivesicular body sorting pathway TAS
    Traceable Author Statement
    more info
    PubMed 
    multivesicular body-lysosome fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    negative regulation of viral release from host cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT nucleus organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    positive regulation of viral release from host cell IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    positive regulation of viral release from host cell IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein heterooligomerization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    protein polymerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    protein transport IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    regulation of centrosome duplication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    NOT regulation of mitotic spindle assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    regulation of viral process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    viral budding via host ESCRT complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    viral budding via host ESCRT complex IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    viral budding via host ESCRT complex TAS
    Traceable Author Statement
    more info
    PubMed 
    viral life cycle TAS
    Traceable Author Statement
    more info
     
    Component Evidence Code Pubs
    ESCRT III complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    ESCRT III complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    ESCRT III complex TAS
    Traceable Author Statement
    more info
    PubMed 
    cytoplasmic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    cytosol TAS
    Traceable Author Statement
    more info
     
    extracellular exosome HDA PubMed 
    late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    multivesicular body IBA
    Inferred from Biological aspect of Ancestor
    more info
    PubMed 
    plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    charged multivesicular body protein 3
    Names
    25.1 protein
    CHMP family, member 3
    chromatin-modifying protein 3
    neuroendocrine differentiation factor
    vacuolar protein sorting 24 homolog
    vacuolar protein sorting-associated protein 24

    NCBI Reference Sequences (RefSeq)

    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_001005753.3NP_001005753.1  charged multivesicular body protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001005753.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate exon in the 5' coding region, compared to variant 1. This results in translation initiation from a downstream start codon and an isoform (2, also known as Vps24beta) that has a shorter N-terminus, compared to isoform 1.
      Source sequence(s)
      AC068288, AF151907, AK290725, DA290886
      Consensus CDS
      CCDS42707.1
      UniProtKB/Swiss-Prot
      Q9Y3E7
      Related
      ENSP00000386590.2, ENST00000409225.2
      Conserved Domains (1) summary
      cl21588
      Location:1121
      Snf7; Snf7
    2. NM_001193517.2NP_001180446.1  charged multivesicular body protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001180446.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in an isoform (3) that is shorter than isoform 1.
      Source sequence(s)
      AC068288, AF151907, AK129502, DA290886
      Consensus CDS
      CCDS54375.1
      UniProtKB/Swiss-Prot
      Q9Y3E7
      Related
      ENSP00000387045.1, ENST00000409727.5
      Conserved Domains (1) summary
      cl21588
      Location:18147
      Snf7; Snf7
    3. NM_016079.4NP_057163.1  charged multivesicular body protein 3 isoform 1

      See identical proteins and their annotated locations for NP_057163.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1, also known as Vps24alpha).
      Source sequence(s)
      AF151907, AK025046, AK312353, BC004419, BU192410, DA290886
      Consensus CDS
      CCDS33236.1
      UniProtKB/Swiss-Prot
      Q9Y3E7
      Related
      ENSP00000263856.4, ENST00000263856.9
      Conserved Domains (1) summary
      pfam03357
      Location:18187
      Snf7; Snf7

    RNA

    1. NR_036454.1 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lack two internal exons in the 5' region, compared to variant 1. This variant is represented as non-coding because it lacks a significant portion of the coding region, as found in variant 1. Translation from the upstream start codon, as found in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AC068288, AF151907, DA046087, DA290886

    RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109

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

    Reference GRCh38.p13 Primary Assembly

    Genomic

    1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

      Range
      86503430..86563497 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
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