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VPS26A VPS26, retromer complex component A [ Homo sapiens (human) ]

Gene ID: 9559, updated on 17-Jun-2019

Summary

Official Symbol
VPS26Aprovided by HGNC
Official Full Name
VPS26, retromer complex component Aprovided by HGNC
Primary source
HGNC:HGNC:12711
See related
Ensembl:ENSG00000122958 MIM:605506
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
HB58; PEP8A; VPS26; Hbeta58
Summary
This gene belongs to a group of vacuolar protein sorting (VPS) genes. The encoded protein is a component of a large multimeric complex, termed the retromer complex, involved in retrograde transport of proteins from endosomes to the trans-Golgi network. The close structural similarity between the yeast and human proteins that make up this complex suggests a similarity in function. Expression studies in yeast and mammalian cells indicate that this protein interacts directly with VPS35, which serves as the core of the retromer complex. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in testis (RPKM 20.4), esophagus (RPKM 15.7) and 25 other tissues See more
Orthologs

Genomic context

See VPS26A in Genome Data Viewer
Location:
10q22.1
Exon count:
10
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 10 NC_000010.11 (69124153..69174416)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 10 NC_000010.10 (70883908..70932617)

Chromosome 10 - NC_000010.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378342 Neighboring gene serglycin Neighboring gene ribosomal protein S12 pseudogene 17 Neighboring gene Suv3 like RNA helicase Neighboring gene uncharacterized LOC101928994 Neighboring gene hexokinase domain containing 1

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?

Phenotypes

NHGRI GWAS Catalog

Description
Genome-wide analysis of polymorphisms associated with cytokine responses in smallpox vaccine recipients.
NHGRI GWA Catalog
Genome-wide association study in individuals of South Asian ancestry identifies six new type 2 diabetes susceptibility loci.
NHGRI GWA Catalog
Identification of HKDC1 and BACE2 as genes influencing glycemic traits during pregnancy through genome-wide association studies.
NHGRI GWA Catalog

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Depletion of VPS26 by siRNA increases plasma membrane expression of HIV-1 gp120/gp41 and incorporation into viral particles, indicating that VPS26 regulates gp120/gp41 trafficking in cells PubMed
Envelope transmembrane glycoprotein gp41 env The gp41 cytoplasmic tail binds directly to retromer components VPS26 and VPS35 in HIV-1-infected cells PubMed
env Depletion of VPS26 by siRNA increases plasma membrane expression of HIV-1 gp120/gp41 and incorporation into viral particles, indicating that VPS26 regulates gp120/gp41 trafficking in cells PubMed
env The gp41 cytoplasmic tail determines sensitivity to VPS26 depletion in HIV-1-infected cells, and the cytoplasmic tail alone is sufficient for trafficking of Env through the retromer-containing compartment PubMed

Go to the HIV-1, Human Interaction Database

Pathways from BioSystems

  • 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...
  • Signal Transduction, organism-specific biosystem (from REACTOME)
    Signal Transduction, organism-specific biosystemSignal transduction is a process in which extracellular signals elicit changes in cell state and activity. Transmembrane receptors sense changes in the cellular environment by binding ligands, such a...
  • Signaling by Wnt, organism-specific biosystem (from REACTOME)
    Signaling by Wnt, organism-specific biosystemWNT signaling pathways control a wide range of developmental and adult process in metozoans including cell proliferation, cell fate decisions, cell polarity and stem cell maintenance (reviewed in Sai...
  • WNT ligand biogenesis and trafficking, organism-specific biosystem (from REACTOME)
    WNT ligand biogenesis and trafficking, organism-specific biosystem19 WNT proteins have been identified in human cells. The WNTs are members of a conserved metazoan family of secreted morphogens that activate several signaling pathways in the responding cell: the c...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ12930

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
Wnt signaling pathway TAS
Traceable Author Statement
more info
 
intracellular protein transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of macroautophagy TAS
Traceable Author Statement
more info
PubMed 
retrograde transport, endosome to Golgi IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retrograde transport, endosome to Golgi IMP
Inferred from Mutant Phenotype
more info
PubMed 
retrograde transport, endosome to Golgi NAS
Non-traceable Author Statement
more info
PubMed 
retrograde transport, endosome to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
cytosol TAS
Traceable Author Statement
more info
 
early endosome 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 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosome IDA
Inferred from Direct Assay
more info
 
retromer complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
retromer complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer complex NAS
Non-traceable Author Statement
more info
PubMed 
retromer, cargo-selective complex IDA
Inferred from Direct Assay
more info
PubMed 
retromer, cargo-selective complex NAS
Non-traceable Author Statement
more info
PubMed 
tubular endosome IDA
Inferred from Direct Assay
more info
PubMed 
vesicle IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vacuolar protein sorting-associated protein 26A
Names
VPS26 retromer complex comonent A
vacuolar protein sorting 26 homolog A
vesicle protein sorting 26A

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_001035260.2NP_001030337.1  vacuolar protein sorting-associated protein 26A isoform 2

    See identical proteins and their annotated locations for NP_001030337.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the 3' coding region which results in a frameshift and early translation termination, compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus, compared to isoform 1.
    Source sequence(s)
    AF054179, AL596223, BQ068008, BX647725, DA498726
    Consensus CDS
    CCDS41536.1
    UniProtKB/Swiss-Prot
    O75436
    Related
    ENSP00000378532.1, ENST00000395098.5
    Conserved Domains (1) summary
    pfam03643
    Location:8243
    Vps26; Vacuolar protein sorting-associated protein 26
  2. NM_001318944.2NP_001305873.1  vacuolar protein sorting-associated protein 26A isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) includes an additional exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (3) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK309021, AL596223, BX647725, DA498726
    Conserved Domains (1) summary
    pfam03643
    Location:45276
    Vps26; Vacuolar protein sorting-associated protein 26
  3. NM_001318945.2NP_001305874.1  vacuolar protein sorting-associated protein 26A isoform 4

    Status: REVIEWED

    Description
    Transcript Variant: This variant (4) includes an additional exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (4) has a shorter and distinct N-terminus, compared to isoform 1.
    Source sequence(s)
    AK297142, AL596223, BX647725, DA498726
    UniProtKB/TrEMBL
    B4DLT1
    Conserved Domains (1) summary
    pfam03643
    Location:34266
    Vps26; Vacuolar protein sorting-associated protein 26
  4. NM_001318946.2NP_001305875.1  vacuolar protein sorting-associated protein 26A isoform 5

    Status: REVIEWED

    Description
    Transcript Variant: This variant (5) lacks an alternate exon in the 5' region, and it thus differs in its 5' UTR and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (5) is shorter at the N-terminus, compared to isoform 1.
    Source sequence(s)
    AF054179, AL596223, BX647725, DA498726
    UniProtKB/Swiss-Prot
    O75436
    Conserved Domains (1) summary
    pfam03643
    Location:1172
    Vps26; Vacuolar protein sorting-associated protein 26
  5. NM_004896.5NP_004887.2  vacuolar protein sorting-associated protein 26A isoform 1

    See identical proteins and their annotated locations for NP_004887.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AF054179, AL596223, BX647725, DA498726
    Consensus CDS
    CCDS7286.1
    UniProtKB/Swiss-Prot
    O75436
    Related
    ENSP00000263559.6, ENST00000263559.11
    Conserved Domains (1) summary
    pfam03643
    Location:8283
    Vps26; Vacuolar protein sorting-associated protein 26

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_000010.11 Reference GRCh38.p13 Primary Assembly

    Range
    69124153..69174416
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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