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

Gene ID: 55823, updated on 18-Jun-2019

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
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
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

Genomic context

See VPS11 in Genome Data Viewer
Location:
11q23.3
Exon count:
16
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 11 NC_000011.10 (119067752..119081978)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 11 NC_000011.9 (118938493..118952688)

Chromosome 11 - NC_000011.10Genomic Context describing neighboring genes Neighboring gene trafficking protein particle complex 4 Neighboring gene solute carrier family 37 member 4 Neighboring gene hypoxia up-regulated 1 Neighboring gene hydroxymethylbilane synthase Neighboring gene H2A histone family member X

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?

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nucleotide binding IEA
Inferred from Electronic Annotation
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
protein binding, bridging IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein domain specific binding IPI
Inferred from Physical Interaction
more info
PubMed 
syntaxin binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
autophagy IEA
Inferred from Electronic Annotation
more info
 
endosomal vesicle fusion IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosome organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome to lysosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
intracellular protein transport IEA
Inferred from Electronic Annotation
more info
 
positive regulation of cellular protein catabolic process IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of early endosome to late endosome transport IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of protein targeting to mitochondrion HMP PubMed 
regulation of SNARE complex assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of organelle assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
regulation of protein stability HMP PubMed 
vacuole organization IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
vesicle docking involved in exocytosis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
HOPS complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
HOPS complex IDA
Inferred from Direct Assay
more info
PubMed 
autophagosome IEA
Inferred from Electronic Annotation
more info
 
clathrin-coated vesicle IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with early endosome IDA
Inferred from Direct Assay
more info
PubMed 
endocytic vesicle IDA
Inferred from Direct Assay
more info
PubMed 
endosome IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with late endosome IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane IEA
Inferred from Electronic Annotation
more info
 
lysosomal membrane HDA PubMed 
lysosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with 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)

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
    4971..19197
    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
    Q9H270
    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_021729.5NP_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 the longer isoform (1).
    Source sequence(s)
    AB027508, AK302973, BC065563, BI561271
    Consensus CDS
    CCDS73404.1
    UniProtKB/Swiss-Prot
    Q9H270
    UniProtKB/TrEMBL
    A0A087WXL6, B7Z879
    Related
    ENSP00000481126.1, ENST00000621676.4
    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 ...

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_000011.10 Reference GRCh38.p13 Primary Assembly

    Range
    119067752..119081978
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011542899.3XP_011541201.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

    See identical proteins and their annotated locations for XP_011541201.1

    Conserved Domains (4) summary
    smart00299
    Location:49173
    CLH; Clathrin heavy chain repeat homology
    cd00162
    Location:459498
    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:55174
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:500545
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
  2. XM_024448607.1XP_024304375.1  vacuolar protein sorting-associated protein 11 homolog isoform X2

    Conserved Domains (2) summary
    pfam12451
    Location:394437
    VPS11_C; Vacuolar protein sorting protein 11 C terminal
    cd16688
    Location:350393
    RING-H2_Vps11; RING finger, H2 subclass, found in vacuolar protein sorting-associated protein 11 homolog (Vps11) and similar proteins
  3. XM_011542898.1XP_011541200.1  vacuolar protein sorting-associated protein 11 homolog isoform X1

    See identical proteins and their annotated locations for XP_011541200.1

    Conserved Domains (4) summary
    smart00299
    Location:49173
    CLH; Clathrin heavy chain repeat homology
    cd00162
    Location:459498
    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:55174
    Clathrin; Region in Clathrin and VPS
    pfam12451
    Location:500545
    VPS11_C; Vacuolar protein sorting protein 11 C terminal

RNA

  1. XR_947859.2 RNA Sequence

    Related
    ENST00000620429.4

Reference GRCh38.p13 PATCHES

Genomic

  1. NW_009646203.1 Reference GRCh38.p13 PATCHES

    Range
    89351..103577
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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