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VPS39 VPS39 subunit of HOPS complex [ Homo sapiens (human) ]

Gene ID: 23339, updated on 17-Jun-2019

Summary

Official Symbol
VPS39provided by HGNC
Official Full Name
VPS39 subunit of HOPS complexprovided by HGNC
Primary source
HGNC:HGNC:20593
See related
Ensembl:ENSG00000166887 MIM:612188
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
TLP; VAM6; hVam6p
Summary
This gene encodes a protein that may promote clustering and fusion of late endosomes and lysosomes. The protein may also act as an adaptor protein that modulates the transforming growth factor-beta response by coupling the transforming growth factor-beta receptor complex to the Smad pathway. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jul 2014]
Expression
Ubiquitous expression in brain (RPKM 16.3), thyroid (RPKM 14.7) and 25 other tissues See more
Orthologs

Genomic context

See VPS39 in Genome Data Viewer
Location:
15q15.1
Exon count:
28
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 15 NC_000015.10 (42158701..42208331, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (42450899..42500524, complement)

Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene phospholipase A2 group IVD Neighboring gene phospholipase A2 group IVF Neighboring gene uncharacterized LOC105370795 Neighboring gene microRNA 627 Neighboring gene transmembrane protein 87A Neighboring gene glucosidase alpha, neutral C Neighboring gene BCL2 interacting protein 3 pseudogene 5

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

Clone Names

  • FLJ21681, FLJ46546, KIAA0770

Gene Ontology Provided by GOA

Process Evidence Code Pubs
autophagy IMP
Inferred from Mutant Phenotype
more info
PubMed 
endosomal vesicle fusion IDA
Inferred from Direct Assay
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
 
late endosome to lysosome transport IDA
Inferred from Direct Assay
more info
PubMed 
retrograde transport, endosome to plasma membrane IMP
Inferred from Mutant Phenotype
more info
PubMed 
vesicle-mediated transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Component Evidence Code Pubs
AP-3 adaptor complex IEA
Inferred from Electronic Annotation
more info
 
HOPS complex IDA
Inferred from Direct Assay
more info
PubMed 
late endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
lysosomal membrane HDA PubMed 
lysosomal membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
lysosomal membrane IDA
Inferred from Direct Assay
more info
PubMed 

General protein information

Preferred Names
vam6/Vps39-like protein
Names
TRAP1-like protein
VPS39, HOPS complex subunit
vacuolar protein sorting 39 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.

mRNA and Protein(s)

  1. NM_001301138.2NP_001288067.1  vam6/Vps39-like protein isoform a

    See identical proteins and their annotated locations for NP_001288067.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).
    Source sequence(s)
    AF280814, AF281052, AK074193, DB461120
    Consensus CDS
    CCDS73710.1
    UniProtKB/Swiss-Prot
    Q96JC1
    Related
    ENSP00000335193.5, ENST00000348544.4
    Conserved Domains (4) summary
    pfam00637
    Location:599746
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:460562
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:772879
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20291
    CNH; CNH domain
  2. NM_015289.4NP_056104.2  vam6/Vps39-like protein isoform b

    See identical proteins and their annotated locations for NP_056104.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an alternate in-frame exon in the 5' coding region, compared to variant 1, resulting in an isoform (b) that is shorter than isoform a.
    Source sequence(s)
    AF281052, AK074193, DB461120
    Consensus CDS
    CCDS10083.1
    UniProtKB/Swiss-Prot
    Q96JC1
    UniProtKB/TrEMBL
    A0A024R9L9
    Related
    ENSP00000326534.5, ENST00000318006.9
    Conserved Domains (4) summary
    pfam10366
    Location:449551
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:761868
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20280
    CNH; CNH domain
    cl26078
    Location:650736
    Clathrin; Region in Clathrin and VPS

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_000015.10 Reference GRCh38.p13 Primary Assembly

    Range
    42158701..42208331 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011521404.2XP_011519706.1  vam6/Vps39-like protein isoform X2

    Conserved Domains (4) summary
    pfam00637
    Location:588735
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:449551
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:761851
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20280
    CNH; CNH domain
  2. XM_017022038.1XP_016877527.1  vam6/Vps39-like protein isoform X5

  3. XM_017022039.1XP_016877528.1  vam6/Vps39-like protein isoform X6

  4. XM_011521403.2XP_011519705.1  vam6/Vps39-like protein isoform X1

    Conserved Domains (4) summary
    pfam00637
    Location:599746
    Clathrin; Region in Clathrin and VPS
    pfam10366
    Location:460562
    Vps39_1; Vacuolar sorting protein 39 domain 1
    pfam10367
    Location:772862
    Vps39_2; Vacuolar sorting protein 39 domain 2
    cl02434
    Location:20291
    CNH; CNH domain
  5. XM_017022037.1XP_016877526.1  vam6/Vps39-like protein isoform X4

  6. XM_017022036.1XP_016877525.1  vam6/Vps39-like protein isoform X3

RNA

  1. XR_001751181.1 RNA Sequence

  2. XR_001751180.1 RNA Sequence

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