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VAC14 VAC14 component of PIKFYVE complex [ Homo sapiens (human) ]

Gene ID: 55697, updated on 17-Jun-2019

Summary

Official Symbol
VAC14provided by HGNC
Official Full Name
VAC14 component of PIKFYVE complexprovided by HGNC
Primary source
HGNC:HGNC:25507
See related
Ensembl:ENSG00000103043 MIM:604632
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
TRX; TAX1BP2; ArPIKfyve
Summary
This gene encodes a scaffold protein that is a component of the PIKfyve protein kinase complex. This complex is responsible for the synthesis of phosphatidylinositol 3,5-bisphosphate, an important component of cellular membranes, from phosphatidylinositol 3-phosphate. Mice lacking a functional copy of this gene exhibit severe neurodegeneration. Mutations in the human gene have been identified in patients with a childhood onset progressive neurological disorder characterized by impaired movement, dystonia, and striatal abnormalities. [provided by RefSeq, May 2017]
Expression
Ubiquitous expression in lymph node (RPKM 2.8), thyroid (RPKM 2.5) and 25 other tissues See more
Orthologs

Genomic context

See VAC14 in Genome Data Viewer
Location:
16q22.1-q22.2
Exon count:
24
Annotation release Status Assembly Chr Location
109.20190607 current GRCh38.p13 (GCF_000001405.39) 16 NC_000016.10 (70687439..70801158, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (70721342..70835074, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene interleukin 34 Neighboring gene MTSS I-BAR domain containing 2 Neighboring gene VAC14 antisense RNA 1 Neighboring gene tRNA-Gly (anticodon GCC) 3-1 Neighboring gene tRNA-Gly (anticodon GCC) 2-4 Neighboring gene tRNA-Gly (anticodon GCC) 5-1 Neighboring gene tRNA-Gly (anticodon GCC) 2-5 Neighboring gene RNA, U6atac small nuclear 25, pseudogene Neighboring gene HYDIN axonemal central pair apparatus protein Neighboring gene uncharacterized LOC102723786 Neighboring gene cap methyltransferase 2

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?

Pathways from BioSystems

  • HTLV-I infection, organism-specific biosystem (from KEGG)
    HTLV-I infection, organism-specific biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • HTLV-I infection, conserved biosystem (from KEGG)
    HTLV-I infection, conserved biosystemHuman T-lymphotropic virus type 1 (HTLV-1) is a pathogenic retrovirus that is associated with adult T-cell leukemia/lymphoma (ATL). It is also strongly implicated in non-neoplastic chronic inflammato...
  • Metabolism, organism-specific biosystem (from REACTOME)
    Metabolism, organism-specific biosystemMetabolic processes in human cells generate energy through the oxidation of molecules consumed in the diet and mediate the synthesis of diverse essential molecules not taken in the diet as well as th...
  • Metabolism of lipids and lipoproteins, organism-specific biosystem (from REACTOME)
    Metabolism of lipids and lipoproteins, organism-specific biosystemLipids are hydrophobic but otherwise chemically diverse molecules that play a wide variety of roles in human biology. They include ketone bodies, fatty acids, triacylglycerols, phospholipids and sphi...
  • PI Metabolism, organism-specific biosystem (from REACTOME)
    PI Metabolism, organism-specific biosystemPhosphatidylinositol (PI), a membrane phospholipid, can be reversibly phosphorylated at the 3, 4, and 5 positions of the inositol ring to generate seven phosphoinositides: phosphatidylinositol 3-phos...
  • Phospholipid metabolism, organism-specific biosystem (from REACTOME)
    Phospholipid metabolism, organism-specific biosystemPhospholipids contain a polar head group and two long-chain fatty acyl moieties, one of which is generally unsaturated. The head group is a glycerol or serine phosphate attached to a polar group such...
  • Synthesis of PIPs at the Golgi membrane, organism-specific biosystem (from REACTOME)
    Synthesis of PIPs at the Golgi membrane, organism-specific biosystemAt the Golgi membrane, phosphatidylinositol 4-phosphate (PI4P) is primarily generated from phosphorylation of phosphatidylinositol (PI). Other phosphoinositides are also generated by the action of v...
  • Synthesis of PIPs at the early endosome membrane, organism-specific biosystem (from REACTOME)
    Synthesis of PIPs at the early endosome membrane, organism-specific biosystemAt the early endosome membrane, phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) is generated in two steps from phosphatidylinositol 3,4-bisphosphate PI(3,4)P2 by the action of various kinases and p...
  • Synthesis of PIPs at the late endosome membrane, organism-specific biosystem (from REACTOME)
    Synthesis of PIPs at the late endosome membrane, organism-specific biosystemAt the late endosome membrane, the primary event is the dephosphorylation of the phosphoinositide phosphatidylinositol 3,5-bisphosphate (PI(3,5)P2) to phosphatidylinositol 3-phosphate (PI3P) and phos...
  • Viral carcinogenesis, organism-specific biosystem (from KEGG)
    Viral carcinogenesis, organism-specific biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...
  • Viral carcinogenesis, conserved biosystem (from KEGG)
    Viral carcinogenesis, conserved biosystemThere is a strong association between viruses and the development of human malignancies. We now know that at least six human viruses, Epstein-Barr virus (EBV), hepatitis B virus (HBV), hepatitis C vi...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ10305, FLJ36622, FLJ46582, MGC149815, MGC149816

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
signaling receptor activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
phosphatidylinositol biosynthetic process IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
phosphatidylinositol biosynthetic process TAS
Traceable Author Statement
more info
 
signal transduction NAS
Non-traceable Author Statement
more info
PubMed 
viral process IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
Golgi membrane TAS
Traceable Author Statement
more info
 
PAS complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
early endosome membrane TAS
Traceable Author Statement
more info
 
endoplasmic reticulum IEA
Inferred from Electronic Annotation
more info
 
endosome membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
endosome membrane IDA
Inferred from Direct Assay
more info
PubMed 
extrinsic component of vacuolar membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
late endosome membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
protein VAC14 homolog
Names
Tax1 (human T-cell leukemia virus type I) binding protein
Vac14, PIKFYVE complex component

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_054902.1 RefSeqGene

    Range
    4994..118731
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001351157.2NP_001338086.1  protein VAC14 homolog isoform 2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR, lacks a portion of the 5' coding region and initiates translation at a downstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AC020763, AC027281, AK307766, AL137396
    Conserved Domains (1) summary
    pfam11916
    Location:308483
    Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
  2. NM_018052.5NP_060522.3  protein VAC14 homolog isoform 1

    See identical proteins and their annotated locations for NP_060522.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK056433, AL137396
    Consensus CDS
    CCDS10896.1
    UniProtKB/Swiss-Prot
    Q08AM6
    Related
    ENSP00000261776.5, ENST00000261776.10
    Conserved Domains (3) summary
    sd00044
    Location:94122
    HEAT; HEAT repeat [structural motif]
    pfam11916
    Location:542717
    Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region

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_000016.10 Reference GRCh38.p13 Primary Assembly

    Range
    70687439..70801158 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_005256038.4XP_005256095.1  protein VAC14 homolog isoform X1

    Conserved Domains (3) summary
    pfam11916
    Location:543717
    Vac14_Fig4_bd; Vacuolar protein 14 C-terminal Fig4p binding
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
    sd00044
    Location:94122
    HEAT; HEAT repeat [structural motif]
  2. XM_017023442.2XP_016878931.1  protein VAC14 homolog isoform X6

  3. XM_017023441.2XP_016878930.1  protein VAC14 homolog isoform X5

  4. XM_011523225.3XP_011521527.1  protein VAC14 homolog isoform X7

    Conserved Domains (2) summary
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
    sd00044
    Location:5378
    HEAT; HEAT repeat [structural motif]
  5. XM_005256041.4XP_005256098.2  protein VAC14 homolog isoform X3

    Conserved Domains (2) summary
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
    sd00044
    Location:5378
    HEAT; HEAT repeat [structural motif]
  6. XM_011523223.3XP_011521525.1  protein VAC14 homolog isoform X2

    Conserved Domains (2) summary
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
    sd00044
    Location:5378
    HEAT; HEAT repeat [structural motif]
  7. XM_011523224.3XP_011521526.1  protein VAC14 homolog isoform X4

    Conserved Domains (2) summary
    pfam12755
    Location:67163
    Vac14_Fab1_bd; Vacuolar 14 Fab1-binding region
    sd00044
    Location:94122
    HEAT; HEAT repeat [structural motif]
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