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ATP6V0D1 ATPase H+ transporting V0 subunit d1 [ Homo sapiens (human) ]

Gene ID: 9114, updated on 6-Oct-2024

Summary

Official Symbol
ATP6V0D1provided by HGNC
Official Full Name
ATPase H+ transporting V0 subunit d1provided by HGNC
Primary source
HGNC:HGNC:13724
See related
Ensembl:ENSG00000159720 MIM:607028; AllianceGenome:HGNC:13724
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
P39; VATX; VMA6; ATP6D; ATP6DV; VPATPD
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 encoded protein is known as the D subunit and is found ubiquitously. [provided by RefSeq, Jul 2008]
Expression
Ubiquitous expression in brain (RPKM 53.8), thyroid (RPKM 41.0) and 25 other tissues See more
Orthologs
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Genomic context

See ATP6V0D1 in Genome Data Viewer
Location:
16q22.1
Exon count:
8
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (67438019..67481157, complement)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (73232795..73275929, complement)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (67471922..67515060, complement)

Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene zinc finger DHHC-type containing 1 Neighboring gene uncharacterized LOC124903702 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67450269-67450926 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67454837-67455408 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67458128-67458722 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67461918-67462452 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67462453-67462987 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7604 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7605 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67469389-67469890 Neighboring gene hydroxysteroid 11-beta dehydrogenase 2 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:67477413-67478036 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67478661-67479284 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67481159-67481658 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67485489-67486172 Neighboring gene Sharpr-MPRA regulatory region 10086 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67495532-67496032 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67499338-67499838 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:67499839-67500339 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10966 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7606 Neighboring gene ATP6V0D1 divergent transcript Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10967 Neighboring gene agouti related neuropeptide Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10968 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:67548235-67548422 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7607 Neighboring gene uncharacterized LOC100505942 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10969 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10971 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10972 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10973 Neighboring gene RHO family interacting cell polarization regulator 1

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues 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 Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Envelope surface glycoprotein gp120 env Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Gag-Pol gag-pol Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Nef nef Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed
Pr55(Gag) gag Tandem affinity purification and mass spectrometry analysis identify V-type proton ATPase subunit d1 (ATP6V0D1; VPATPD), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells PubMed

Go to the HIV-1, Human Interaction Database

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ43534

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
enables protein-containing complex binding IEA
Inferred from Electronic Annotation
more info
 
enables proton-transporting ATPase activity, rotational mechanism IEA
Inferred from Electronic Annotation
more info
 
Process Evidence Code Pubs
involved_in cellular response to increased oxygen levels IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in cilium assembly ISS
Inferred from Sequence or Structural Similarity
more info
 
involved_in intracellular iron ion homeostasis IMP
Inferred from Mutant Phenotype
more info
PubMed 
involved_in proton transmembrane transport NAS
Non-traceable Author Statement
more info
PubMed 
involved_in regulation of macroautophagy NAS
Non-traceable Author Statement
more info
PubMed 
involved_in synaptic vesicle lumen acidification IEA
Inferred from Electronic Annotation
more info
 
involved_in vacuolar acidification IBA
Inferred from Biological aspect of Ancestor
more info
 
involved_in vacuolar transport IBA
Inferred from Biological aspect of Ancestor
more info
 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
 
located_in axon terminus IEA
Inferred from Electronic Annotation
more info
 
colocalizes_with centrosome IDA
Inferred from Direct Assay
more info
PubMed 
located_in clathrin-coated vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
is_active_in early endosome IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in endosome membrane TAS
Traceable Author Statement
more info
 
located_in extracellular exosome HDA PubMed 
located_in lysosomal membrane HDA PubMed 
located_in lysosomal membrane TAS
Traceable Author Statement
more info
 
located_in membrane IDA
Inferred from Direct Assay
more info
PubMed 
located_in phagocytic vesicle membrane TAS
Traceable Author Statement
more info
 
part_of plasma membrane proton-transporting V-type ATPase complex IBA
Inferred from Biological aspect of Ancestor
more info
 
located_in synaptic vesicle membrane IEA
Inferred from Electronic Annotation
more info
 
part_of vacuolar proton-transporting V-type ATPase complex IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of vacuolar proton-transporting V-type ATPase complex IDA
Inferred from Direct Assay
more info
PubMed 
part_of vacuolar proton-transporting V-type ATPase complex NAS
Non-traceable Author Statement
more info
PubMed 
part_of vacuolar proton-transporting V-type ATPase, V0 domain ISS
Inferred from Sequence or Structural Similarity
more info
 

General protein information

Preferred Names
V-type proton ATPase subunit d 1
Names
32 kDa accessory protein
ATPase, H+ transporting, lysosomal (vacuolar proton pump), member D
ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d1
H(+)-transporting two-sector ATPase, subunit D
V-ATPase 40 KDa accessory protein
V-ATPase AC39 subunit
V-ATPase subunit d 1
V-ATPase, subunit D
vacuolar proton pump subunit d 1
NP_004682.2

NCBI Reference Sequences (RefSeq)

NEW Try the new Transcript table

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_011482.1 RefSeqGene

    Range
    5030..48168
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_004691.5NP_004682.2  V-type proton ATPase subunit d 1

    See identical proteins and their annotated locations for NP_004682.2

    Status: REVIEWED

    Source sequence(s)
    BC008861, BM677562
    Consensus CDS
    CCDS10838.1
    UniProtKB/Swiss-Prot
    P12953, P61421, Q02547
    UniProtKB/TrEMBL
    B2R7M1
    Related
    ENSP00000290949.3, ENST00000290949.8
    Conserved Domains (1) summary
    pfam01992
    Location:16344
    vATP-synt_AC39; ATP synthase (C/AC39) subunit

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000016.10 Reference GRCh38.p14 Primary Assembly

    Range
    67438019..67481157 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060940.1 Alternate T2T-CHM13v2.0

    Range
    73232795..73275929 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)