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    VPS11 VPS11 core subunit of CORVET and HOPS complexes [ Homo sapiens (human) ]

    Gene ID: 55823, updated on 5-May-2024

    Summary

    Official Symbol
    VPS11provided by HGNC
    Official Full Name
    VPS11 core subunit of CORVET and HOPS complexesprovided by HGNC
    Primary source
    HGNC:HGNC:14583
    See related
    Ensembl:ENSG00000160695 MIM:608549; AllianceGenome:HGNC:14583
    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
    END1; PEP5; HLD12; RNF108; hVPS11; HLD12; DYT32
    Summary
    Vesicle mediated protein sorting plays an important role in segregation of intracellular molecules into distinct organelles. Genetic studies in yeast have identified more than 40 vacuolar protein sorting (VPS) genes involved in vesicle transport to vacuoles. This gene encodes the human homolog of yeast class C Vps11 protein. The mammalian class C Vps proteins are predominantly associated with late endosomes/lysosomes, and like their yeast counterparts, may mediate vesicle trafficking steps in the endosome/lysosome pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2014]
    Expression
    Ubiquitous expression in thyroid (RPKM 16.0), bone marrow (RPKM 14.4) and 25 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See VPS11 in Genome Data Viewer
    Location:
    11q23.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 11 NC_000011.10 (119067818..119081972)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 11 NC_060935.1 (119088176..119102362)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118938529..118952682)

    Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene HYOU1 antisense RNA 1 Neighboring gene hypoxia up-regulated 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5617 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927013-118927514 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118927515-118928014 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5618 Neighboring gene uncharacterized LOC124902769 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 5620 Neighboring gene H3K27ac hESC enhancer GRCh37_chr11:118955192-118955889 Neighboring gene hydroxymethylbilane synthase Neighboring gene H3K4me1 hESC enhancer GRCh37_chr11:118963458-118963970 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965105-118965668 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr11:118965669-118966232 Neighboring gene dolichyl-phosphate N-acetylglucosaminephosphotransferase 1 Neighboring gene H2A.X variant histone

    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 Functions

    What's a GeneRIF?

    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 metal ion binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
     
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein domain specific binding IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    enables protein-macromolecule adaptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables syntaxin binding IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables ubiquitin protein ligase activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in autophagy IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in endosomal vesicle fusion IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in endosomal vesicle fusion NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in endosome organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in endosome to lysosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in intracellular protein transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in negative regulation of intracellular estrogen receptor signaling pathway IGI
    Inferred from Genetic Interaction
    more info
    PubMed 
    involved_in organelle fusion IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in positive regulation of early endosome to late endosome transport IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein catabolic process IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in positive regulation of protein targeting to mitochondrion HMP PubMed 
    involved_in protein ubiquitination IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of SNARE complex assembly NAS
    Non-traceable Author Statement
    more info
    PubMed 
    involved_in regulation of organelle assembly IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in regulation of protein stability HMP PubMed 
    involved_in vacuole organization IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in vesicle docking involved in exocytosis IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    Component Evidence Code Pubs
    part_of CORVET complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    part_of HOPS complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of HOPS complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    part_of HOPS complex NAS
    Non-traceable Author Statement
    more info
    PubMed 
    located_in autophagosome IEA
    Inferred from Electronic Annotation
    more info
     
    located_in clathrin-coated vesicle IEA
    Inferred from Electronic Annotation
    more info
     
    colocalizes_with early endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endocytic vesicle IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in endosome membrane TAS
    Traceable Author Statement
    more info
     
    colocalizes_with late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in late endosome membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in lysosomal membrane HDA PubMed 
    colocalizes_with lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 
    located_in lysosome IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

    Preferred Names
    vacuolar protein sorting-associated protein 11 homolog
    Names
    RING finger protein 108
    VPS11, CORVET/HOPS core subunit
    vacuolar protein sorting 11 homolog

    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.

    Genomic

    1. NG_029670.2 RefSeqGene

      Range
      5037..19191
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001290185.2NP_001277114.1  vacuolar protein sorting-associated protein 11 homolog isoform 2

      See identical proteins and their annotated locations for NP_001277114.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in its 5' UTR and 5' coding region, and uses an alternate start codon, compared to variant 1. The encoded isoform (2) has a shorter and distinct N-terminus, compared to isoform 1.
      Source sequence(s)
      AK302973, BC065563, BI561271
      Consensus CDS
      CCDS76485.1
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      UniProtKB/TrEMBL
      B7Z879
      Related
      ENSP00000481807.1, ENST00000614944.4
      Conserved Domains (5) summary
      smart00299
      Location:401525
      CLH; Clathrin heavy chain repeat homology
      cd00162
      Location:811850
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam00637
      Location:407526
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:852897
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl02567
      Location:132282
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    2. NM_001378218.1NP_001365147.1  vacuolar protein sorting-associated protein 11 homolog isoform 3

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      Conserved Domains (4) summary
      cd16688
      Location:824867
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:415540
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:868911
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl29593
      Location:146296
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    3. NM_001378219.1NP_001365148.1  vacuolar protein sorting-associated protein 11 homolog isoform 4

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      Conserved Domains (4) summary
      cd16688
      Location:824867
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:421540
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:868911
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl29593
      Location:142292
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    4. NM_001378220.1NP_001365149.1  vacuolar protein sorting-associated protein 11 homolog isoform 5

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      Conserved Domains (4) summary
      cd16688
      Location:815858
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:406531
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:859902
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl29593
      Location:142292
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    5. NM_001378221.1NP_001365150.1  vacuolar protein sorting-associated protein 11 homolog isoform 6

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      Conserved Domains (4) summary
      cd16688
      Location:814857
      RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
      pfam00637
      Location:405530
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:858901
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl29593
      Location:136286
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...
    6. NM_021729.6NP_068375.3  vacuolar protein sorting-associated protein 11 homolog isoform 1

      See identical proteins and their annotated locations for NP_068375.3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AP003392, KF511489
      Consensus CDS
      CCDS73404.1
      UniProtKB/Swiss-Prot
      Q8WY89, Q96EP8, Q9H270, Q9H6D9, Q9HCS6
      UniProtKB/TrEMBL
      A0A087WXL6
      Related
      ENSP00000481126.1, ENST00000621676.5
      Conserved Domains (5) summary
      smart00299
      Location:411535
      CLH; Clathrin heavy chain repeat homology
      cd00162
      Location:821860
      RING; RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in ...
      pfam00637
      Location:417536
      Clathrin; Region in Clathrin and VPS
      pfam12451
      Location:862907
      VPS11_C; Vacuolar protein sorting protein 11 C terminal
      cl02567
      Location:142292
      WD40; WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from ...

    RNA

    1. NR_165447.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    2. NR_165448.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    3. NR_165449.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    4. NR_165450.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
      Related
      ENST00000622309.4
    5. NR_165451.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    6. NR_165452.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    7. NR_165453.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489
    8. NR_165454.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AP003392, KF511489

    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_000011.10 Reference GRCh38.p14 Primary Assembly

      Range
      119067818..119081972
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047427256.1XP_047283212.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

    RNA

    1. XR_947859.3 RNA Sequence

    Reference GRCh38.p14 PATCHES

    Genomic

    1. NW_009646203.1 Reference GRCh38.p14 PATCHES

      Range
      89417..103571
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054331618.1XP_054187593.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

    RNA

    1. XR_008485725.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060935.1 Alternate T2T-CHM13v2.0

      Range
      119088176..119102362
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054369352.1XP_054225327.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

    RNA

    1. XR_008488420.1 RNA Sequence