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ATP6V1D ATPase H+ transporting V1 subunit D [ Homo sapiens (human) ]

Gene ID: 51382, updated on 2-Oct-2018

Summary

Official Symbol
ATP6V1Dprovided by HGNC
Official Full Name
ATPase H+ transporting V1 subunit Dprovided by HGNC
Primary source
HGNC:HGNC:13527
See related
Ensembl:ENSG00000100554 MIM:609398; Vega:OTTHUMG00000171244
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
VATD; VMA8; ATP6M
Summary
This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. V-ATPase dependent organelle acidification is necessary for such intracellular processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. V-ATPase is composed of a cytosolic V1 domain and a transmembrane V0 domain. The V1 domain consists of three A and three B subunits, two G subunits plus the C, D, E, F, and H subunits. The V1 domain contains the ATP catalytic site. The V0 domain consists of five different subunits: a, c, c', c", and d. Additional isoforms of many of the V1 and V0 subunit proteins are encoded by multiple genes or alternatively spliced transcript variants. This gene encodes the V1 domain D subunit protein. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in adrenal (RPKM 49.7), brain (RPKM 46.5) and 25 other tissues See more
Orthologs

Genomic context

See ATP6V1D in Genome Data Viewer
Location:
14q23.3
Exon count:
9
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 14 NC_000014.9 (67337864..67360003, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (67804581..67826720, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene gephyrin Neighboring gene splicing factor 3b, subunit 4 pseudogene 1 Neighboring gene family with sequence similarity 71 member D Neighboring gene membrane palmitoylated protein 5 Neighboring gene eukaryotic translation initiation factor 2 subunit alpha Neighboring gene pleckstrin 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Pathways from BioSystems

  • Collecting duct acid secretion, organism-specific biosystem (from KEGG)
    Collecting duct acid secretion, organism-specific biosystemOne of the important roles of the collecting duct segment of the kidney nephron is acid secretion. As daily food intake loads acid into the body, urinary acid excretion is essential, and urine pH can...
  • Collecting duct acid secretion, conserved biosystem (from KEGG)
    Collecting duct acid secretion, conserved biosystemOne of the important roles of the collecting duct segment of the kidney nephron is acid secretion. As daily food intake loads acid into the body, urinary acid excretion is essential, and urine pH can...
  • Epithelial cell signaling in Helicobacter pylori infection, organism-specific biosystem (from KEGG)
    Epithelial cell signaling in Helicobacter pylori infection, organism-specific biosystemTwo major virulence factors of H. pylori are the vacuolating cytotoxin (VacA) and the cag type-IV secretion system (T4SS) and its translocated effector protein, cytotoxin-associated antigen A (CagA)....
  • Epithelial cell signaling in Helicobacter pylori infection, conserved biosystem (from KEGG)
    Epithelial cell signaling in Helicobacter pylori infection, conserved biosystemTwo major virulence factors of H. pylori are the vacuolating cytotoxin (VacA) and the cag type-IV secretion system (T4SS) and its translocated effector protein, cytotoxin-associated antigen A (CagA)....
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • Insulin receptor recycling, organism-specific biosystem (from REACTOME)
    Insulin receptor recycling, organism-specific biosystemTriggered by acidification of the endosome, insulin dissociates from the receptor and is degraded. The receptor is dephosphorylated and re-integrated into the plasma membrane, ready to be activated a...
  • Ion channel transport, organism-specific biosystem (from REACTOME)
    Ion channel transport, organism-specific biosystemIon channels mediate the flow of ions across the plasma membrane of cells. They are integral membrane proteins, typically a multimer of proteins, which, when arranged in the membrane, create a pore f...
  • Iron uptake and transport, organism-specific biosystem (from REACTOME)
    Iron uptake and transport, organism-specific biosystemThe transport of iron between cells is mediated by transferrin. However, iron can also enter and leave cells not only by itself, but also in the form of heme and siderophores. When entering the cell ...
  • Metabolic pathways, organism-specific biosystem (from KEGG)
    Metabolic pathways, organism-specific biosystem
    Metabolic pathways
  • Neutrophil degranulation, organism-specific biosystem (from REACTOME)
    Neutrophil degranulation, organism-specific biosystemNeutrophils are the most abundant leukocytes (white blood cells), indispensable in defending the body against invading microorganisms. In response to infection, neutrophils leave the circulation and ...
  • Oxidative phosphorylation, organism-specific biosystem (from KEGG)
    Oxidative phosphorylation, organism-specific biosystem
    Oxidative phosphorylation
  • Oxidative phosphorylation, conserved biosystem (from KEGG)
    Oxidative phosphorylation, conserved biosystem
    Oxidative phosphorylation
  • Phagosome, organism-specific biosystem (from KEGG)
    Phagosome, organism-specific biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • Phagosome, conserved biosystem (from KEGG)
    Phagosome, conserved biosystemPhagocytosis is the process of taking in relatively large particles by a cell, and is a central mechanism in the tissue remodeling, inflammation, and defense against infectious agents. A phagosome is...
  • ROS, RNS production in phagocytes, organism-specific biosystem (from REACTOME)
    ROS, RNS production in phagocytes, organism-specific biosystemThe first line of defense against infectious agents involves an active recruitment of phagocytes to the site of infection. Recruited cells include polymorhonuclear (PMN) leukocytes (i.e., neutrophils...
  • Rheumatoid arthritis, organism-specific biosystem (from KEGG)
    Rheumatoid arthritis, organism-specific biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
  • Rheumatoid arthritis, conserved biosystem (from KEGG)
    Rheumatoid arthritis, conserved biosystemRheumatoid arthritis (RA) is a chronic autoimmune joint disease where persistent inflammation affects bone remodeling leading to progressive bone destruction. In RA, abnormal activation of the immune...
  • 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 Insulin receptor, organism-specific biosystem (from REACTOME)
    Signaling by Insulin receptor, organism-specific biosystemInsulin binding to its receptor results in receptor autophosphorylation on tyrosine residues and the tyrosine phosphorylation of insulin receptor substrates (e.g. IRS and Shc) by the insulin receptor...
  • Synaptic vesicle cycle, organism-specific biosystem (from KEGG)
    Synaptic vesicle cycle, organism-specific biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
  • Synaptic vesicle cycle, conserved biosystem (from KEGG)
    Synaptic vesicle cycle, conserved biosystemCommunication between neurons is mediated by the release of neurotransmitter from synaptic vesicles (SVs). At the nerve terminal, SVs cycle through repetitive episodes of exocytosis and endocytosis. ...
  • Transferrin endocytosis and recycling, organism-specific biosystem (from REACTOME)
    Transferrin endocytosis and recycling, organism-specific biosystemEndocytosis of iron loaded transferrin/receptor complex leads, after acidification of the endosome, to the separation of iron and its diffusion out of the vesicle. The endosome is not fused with a ly...
  • Transmembrane transport of small molecules, organism-specific biosystem (from REACTOME)
    Transmembrane transport of small molecules, organism-specific biosystem
    Transmembrane transport of small molecules
  • V-type ATPase, eukaryotes, organism-specific biosystem (from KEGG)
    V-type ATPase, eukaryotes, organism-specific biosystemStructural complex; Energy metabolism; ATP synthesis
  • V-type ATPase, eukaryotes, conserved biosystem (from KEGG)
    V-type ATPase, eukaryotes, conserved biosystemStructural complex; Energy metabolism; ATP synthesis
  • Vibrio cholerae infection, organism-specific biosystem (from KEGG)
    Vibrio cholerae infection, organism-specific biosystemCholera toxin (CTX) is one of the main virulence factors of Vibrio cholerae. Once secreted, CTX B-chain (CTXB) binds to ganglioside GM1 on the surface of the host's cells. After binding takes place, ...
  • Vibrio cholerae infection, conserved biosystem (from KEGG)
    Vibrio cholerae infection, conserved biosystemCholera toxin (CTX) is one of the main virulence factors of Vibrio cholerae. Once secreted, CTX B-chain (CTXB) binds to ganglioside GM1 on the surface of the host's cells. After binding takes place, ...
  • mTOR signaling pathway, organism-specific biosystem (from KEGG)
    mTOR signaling pathway, organism-specific biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...
  • mTOR signaling pathway, conserved biosystem (from KEGG)
    mTOR signaling pathway, conserved biosystemThe mammalian (mechanistic) target of rapamycin (mTOR) is a highly conserved serine/threonine protein kinase, which exists in two complexes termed mTOR complex 1 (mTORC1) and 2 (mTORC2). mTORC1 conta...

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
protein binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
proton-transporting ATPase activity, rotational mechanism IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
cilium assembly IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cilium assembly IMP
Inferred from Mutant Phenotype
more info
PubMed 
insulin receptor signaling pathway TAS
Traceable Author Statement
more info
 
ion transmembrane transport TAS
Traceable Author Statement
more info
 
neutrophil degranulation TAS
Traceable Author Statement
more info
 
protein localization to cilium IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
protein localization to cilium IMP
Inferred from Mutant Phenotype
more info
PubMed 
proton transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
regulation of macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
transferrin transport TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
PubMed 
colocalizes_with cilium IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
extracellular exosome HDA PubMed 
lysosomal membrane HDA PubMed 
membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
plasma membrane TAS
Traceable Author Statement
more info
 
proton-transporting V-type ATPase complex IDA
Inferred from Direct Assay
more info
PubMed 
specific granule membrane TAS
Traceable Author Statement
more info
 

General protein information

Preferred Names
V-type proton ATPase subunit D
Names
ATPase, H+ transporting lysosomal, member M
ATPase, H+ transporting, lysosomal (vacuolar proton pump)
ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D
H(+)-transporting two-sector ATPase, subunit M
V-ATPase 28 kDa accessory protein
V-ATPase D subunit
V-ATPase subunit D
vacuolar ATP synthase subunit D
vacuolar H-ATPase subunit D
vacuolar proton pump D subunit
vacuolar proton pump delta polypeptide
vacuolar proton pump subunit D
vacuolar proton-ATPase subunit D
NP_057078.1

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_015994.3NP_057078.1  V-type proton ATPase subunit D

    See identical proteins and their annotated locations for NP_057078.1

    Status: REVIEWED

    Source sequence(s)
    AL139785, BC001411, BU726615, DB039102
    Consensus CDS
    CCDS9780.1
    UniProtKB/Swiss-Prot
    Q9Y5K8
    UniProtKB/TrEMBL
    A0A024R683
    Related
    ENSP00000216442.7, OTTHUMP00000245549, ENST00000216442.11, OTTHUMT00000412511
    Conserved Domains (1) summary
    pfam01813
    Location:15207
    ATP-synt_D; ATP synthase subunit D

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 109 details...Open this link in a new tab

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000014.9 Reference GRCh38.p12 Primary Assembly

    Range
    67337864..67360003 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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