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    VPS4B vacuolar protein sorting 4 homolog B [ Homo sapiens (human) ]

    Gene ID: 9525, updated on 28-Oct-2024

    Summary

    Official Symbol
    VPS4Bprovided by HGNC
    Official Full Name
    vacuolar protein sorting 4 homolog Bprovided by HGNC
    Primary source
    HGNC:HGNC:10895
    See related
    Ensembl:ENSG00000119541 MIM:609983; AllianceGenome:HGNC:10895
    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
    MIG1; SKD1; SKD1B; VPS4-2
    Summary
    The protein encoded by this gene is a member of the AAA protein family (ATPases associated with diverse cellular activities), and is the homolog of the yeast Vps4 protein. In humans, two paralogs of the yeast protein have been identified. The former share a high degree of aa sequence similarity with each other, and also with yeast Vps4 and mouse Skd1 proteins. Mouse Skd1 (suppressor of K+ transport defect 1) has been shown to be a yeast Vps4 ortholog. Functional studies indicate that both human paralogs associate with the endosomal compartments, and are involved in intracellular protein trafficking, similar to Vps4 protein in yeast. The gene encoding this paralog has been mapped to chromosome 18; the gene for the other resides on chromosome 16. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in esophagus (RPKM 35.7), colon (RPKM 23.8) and 25 other tissues See more
    Orthologs
    NEW
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    Genomic context

    See VPS4B in Genome Data Viewer
    Location:
    18q21.33
    Exon count:
    11
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 18 NC_000018.10 (63389190..63422476, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 18 NC_060942.1 (63594233..63627515, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 18 NC_000018.9 (61056423..61089709, complement)

    Chromosome 18 - NC_000018.10Genomic Context describing neighboring genes Neighboring gene 3-ketodihydrosphingosine reductase Neighboring gene uncharacterized LOC124904317 Neighboring gene Sharpr-MPRA regulatory region 13815 Neighboring gene H3K27ac hESC enhancer GRCh37_chr18:61033863-61034810 Neighboring gene KDSR divergent transcript Neighboring gene uncharacterized LOC124904316 Neighboring gene proteasome 26S subunit, ATPase 5 pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 13468 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:61094350-61095549 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 9530 Neighboring gene VPS4B-SERPINB5 intergenic CAGE-defined mid-level expression enhancer Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr18:61134418-61135617 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr18:61142940-61144139 Neighboring gene serpin family B member 5 Neighboring gene ATP synthase membrane subunit c locus 1 pseudogene 6 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr18:61178432-61178952 Neighboring gene serpin family B member 12

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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 Functions

    What's a GeneRIF?

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Nef nef HIV-1 Nef targets CD4 to CD63-containing lysosomes for Nef-induced degradation of CD4, which requires the VPS4-mediated ESCRT machinery PubMed
    Pr55(Gag) gag ALIX, CHMP2A/B, CHMP4A/B, and VPS4A/B proteins are required for the budding of HIV-1 Gag and the HIV-1 infectivity PubMed
    gag VPS4A/B proteins are recruited to assist with membrane fission after full assembly of HIV-1 Gag into the VLP PubMed
    gag ISG15 inhibits budding of HIV-1 by disrupting the association between Vps4 and the Gag budding complex PubMed
    gag The budding defect of p6-deficient HIV-1 Gag is caused primarily by C-terminal exposure of p1. The p1 domain of p6-deficient Gag acts as an inhibitory budding signal by blocking the interaction of Gag with CD63 and VPS4B PubMed
    Vpu vpu The v-ATPase VPS4 is required for Vpu-induced cell surface downregulation of BST-2. VPS4 E223/Q mutant impairs the ability of Vpu to downregulate BST-2 from the cell surface PubMed
    p1 gag The budding defect of p6-deficient HIV-1 Gag is caused primarily by C-terminal exposure of p1, which activates a cis-acting inhibitory budding signal (IBS) and impairs exosomes and microvesicles (EMV) cargo-VPS4 interaction PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP hydrolysis activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables ATP hydrolysis activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables identical protein binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein homodimerization activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables protein-containing complex binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in ESCRT III complex disassembly IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in ESCRT III complex disassembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in angiogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in autophagosome maturation NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in autophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in canonical Wnt signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cholesterol transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endosomal transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    acts_upstream_of_or_within endosomal transport IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in endosome to lysosome transport via multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in establishment of blood-brain barrier IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in late endosomal microautophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in late endosome to lysosome transport via multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in macroautophagy NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in membrane fission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in midbody abscission IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in midbody abscission NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in mitotic metaphase chromosome alignment IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in multivesicular body assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in multivesicular body sorting pathway NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in negative regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nuclear membrane reassembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in nucleus organization IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in nucleus organization NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in plasma membrane repair NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in positive regulation of G2/M transition of mitotic cell cycle IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of centriole elongation IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of exosomal secretion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in potassium ion transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in protein depolymerization IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in regulation of centrosome duplication IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of mitotic spindle assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in response to lipid IDA
    Inferred from Direct Assay
    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 ubiquitin-independent protein catabolic process via the multivesicular body sorting pathway IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in vacuole organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in viral budding from plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in viral budding via host ESCRT complex IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    Component Evidence Code Pubs
    part_of ATPase complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in Flemming body IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in centrosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in cytoplasm 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 endosome membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in extracellular exosome HDA PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in midbody NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of nuclear pore NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in plasma membrane NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in spindle pole IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 4B
    Names
    cell migration-inducing 1
    cell migration-inducing gene 1 protein
    suppressor of K(+) transport growth defect 1
    suppressor of K+ transport defect 1
    vacuolar protein sorting 4B
    NP_004860.2
    XP_047293905.1
    XP_054175353.1

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_004869.4NP_004860.2  vacuolar protein sorting-associated protein 4B

      See identical proteins and their annotated locations for NP_004860.2

      Status: REVIEWED

      Source sequence(s)
      AF195514, DA306069
      Consensus CDS
      CCDS11983.1
      UniProtKB/Swiss-Prot
      O75351, Q69HW4, Q9GZS7
      UniProtKB/TrEMBL
      A8K4G7
      Related
      ENSP00000238497.4, ENST00000238497.10
      Conserved Domains (3) summary
      COG0464
      Location:124355
      SpoVK; AAA+-type ATPase, SpoVK/Ycf46/Vps4 family [Cell wall/membrane/envelope biogenesis, Cell cycle control, cell division, chromosome partitioning, Signal transduction mechanisms]
      cd02678
      Location:681
      MIT_VPS4; MIT: domain contained within Microtubule Interacting and Trafficking molecules. This sub-family of MIT domains is found in intracellular protein transport proteins of the AAA-ATPase family. The molecular function of the MIT domain is unclear.
      pfam09336
      Location:381441
      Vps4_C; Vps4 C terminal oligomerization domain

    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_000018.10 Reference GRCh38.p14 Primary Assembly

      Range
      63389190..63422476 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047437949.1XP_047293905.1  vacuolar protein sorting-associated protein 4B isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060942.1 Alternate T2T-CHM13v2.0

      Range
      63594233..63627515 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054319378.1XP_054175353.1  vacuolar protein sorting-associated protein 4B isoform X1