Human Gene ATP6V0D2 (uc003ydp.1) Description and Page Index
  Description: Homo sapiens ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2 (ATP6V0D2), mRNA.
Transcript (Including UTRs)
   Position: hg19 chr8:87,111,139-87,166,454 Size: 55,316 Total Exon Count: 8 Strand: +
Coding Region
   Position: hg19 chr8:87,111,208-87,165,206 Size: 53,999 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsMalaCardsCTDGene Alleles
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:87,111,139-87,166,454)mRNA (may differ from genome)Protein (350 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: VA0D2_HUMAN
DESCRIPTION: RecName: Full=V-type proton ATPase subunit d 2; Short=V-ATPase subunit d 2; AltName: Full=Vacuolar proton pump subunit d 2;
FUNCTION: Subunit of the integral membrane V0 complex of vacuolar ATPase. Vacuolar ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells, thus providing most of the energy required for transport processes in the vacuolar system. May play a role in coupling of proton transport and ATP hydrolysis (By similarity).
SUBUNIT: V-ATPase is a heteromultimeric enzyme composed of a peripheral catalytic V1 complex (components A to H) attached to an integral membrane V0 proton pore complex (components: a, c, c', c'' and d).
TISSUE SPECIFICITY: Kidney, osteoclast and lung.
SIMILARITY: Belongs to the V-ATPase V0D/AC39 subunit family.

-  MalaCards Disease Associations
  MalaCards Gene Search: ATP6V0D2
Diseases sorted by gene-association score: neurotic disorder (5)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 21.24 RPKM in Kidney - Cortex
Total median expression: 23.46 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -12.7069-0.184 Picture PostScript Text
3' UTR -321.611248-0.258 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR016727 - ATPase_V0-cplx_dsu
IPR002843 - ATPase_V0/A0-cplx_csu/dsu

Pfam Domains:
PF01992 - ATP synthase (C/AC39) subunit

SCOP Domains:
103486 - V-type ATP synthase subunit C

ModBase Predicted Comparative 3D Structure on Q8N8Y2
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008553 hydrogen-exporting ATPase activity, phosphorylative mechanism
GO:0015078 hydrogen ion transmembrane transporter activity
GO:0046961 proton-transporting ATPase activity, rotational mechanism

Biological Process:
GO:0006811 ion transport
GO:0007034 vacuolar transport
GO:0007035 vacuolar acidification
GO:0008286 insulin receptor signaling pathway
GO:0015991 ATP hydrolysis coupled proton transport
GO:0016241 regulation of macroautophagy
GO:0033572 transferrin transport
GO:0034220 ion transmembrane transport

Cellular Component:
GO:0005765 lysosomal membrane
GO:0005768 endosome
GO:0005769 early endosome
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016324 apical plasma membrane
GO:0016471 vacuolar proton-transporting V-type ATPase complex
GO:0030670 phagocytic vesicle membrane
GO:0033179 proton-transporting V-type ATPase, V0 domain
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  KJ895887 - Synthetic construct Homo sapiens clone ccsbBroadEn_05281 ATP6V0D2 gene, encodes complete protein.
BC065207 - Homo sapiens ATPase, H+ transporting, lysosomal 38kDa, V0 subunit d2, mRNA (cDNA clone MGC:70491 IMAGE:5190344), complete cds.
AK096027 - Homo sapiens cDNA FLJ38708 fis, clone KIDNE2002872, moderately similar to Mus musculus Ac39/physophilin mRNA.
AY079172 - Homo sapiens vacuolar H+ ATPase d2 subunit (ATP6V0D2) mRNA, complete cds.
JD239683 - Sequence 220707 from Patent EP1572962.
JD237046 - Sequence 218070 from Patent EP1572962.
JD373991 - Sequence 355015 from Patent EP1572962.
JD078603 - Sequence 59627 from Patent EP1572962.
JD325901 - Sequence 306925 from Patent EP1572962.
JD153107 - Sequence 134131 from Patent EP1572962.
JD246407 - Sequence 227431 from Patent EP1572962.
JD351083 - Sequence 332107 from Patent EP1572962.
JD513034 - Sequence 494058 from Patent EP1572962.
JD317667 - Sequence 298691 from Patent EP1572962.
JD337715 - Sequence 318739 from Patent EP1572962.
JD252525 - Sequence 233549 from Patent EP1572962.
JD094874 - Sequence 75898 from Patent EP1572962.
JD480582 - Sequence 461606 from Patent EP1572962.
JD397170 - Sequence 378194 from Patent EP1572962.
JD415058 - Sequence 396082 from Patent EP1572962.
JD347748 - Sequence 328772 from Patent EP1572962.
JD277532 - Sequence 258556 from Patent EP1572962.
JD207722 - Sequence 188746 from Patent EP1572962.
JD239234 - Sequence 220258 from Patent EP1572962.
JD268997 - Sequence 250021 from Patent EP1572962.
JD282415 - Sequence 263439 from Patent EP1572962.
JD507824 - Sequence 488848 from Patent EP1572962.
JD301273 - Sequence 282297 from Patent EP1572962.
JD252326 - Sequence 233350 from Patent EP1572962.
JD382856 - Sequence 363880 from Patent EP1572962.
JD242936 - Sequence 223960 from Patent EP1572962.
JD414897 - Sequence 395921 from Patent EP1572962.
JD503281 - Sequence 484305 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa00190 - Oxidative phosphorylation
hsa01100 - Metabolic pathways
hsa04142 - Lysosome
hsa04966 - Collecting duct acid secretion
hsa05110 - Vibrio cholerae infection
hsa05120 - Epithelial cell signaling in Helicobacter pylori infection

Reactome (by CSHL, EBI, and GO)

Protein Q8N8Y2 (Reactome details) participates in the following event(s):

R-HSA-5252133 ATP6AP1 binds V-ATPase
R-HSA-1222516 Intraphagosomal pH is lowered to 5 by V-ATPase
R-HSA-74723 Endosome acidification
R-HSA-917841 Acidification of Tf:TfR1 containing endosome
R-HSA-77387 Insulin receptor recycling
R-HSA-917977 Transferrin endocytosis and recycling
R-HSA-983712 Ion channel transport
R-HSA-74752 Signaling by Insulin receptor
R-HSA-917937 Iron uptake and transport
R-HSA-382551 Transport of small molecules
R-HSA-1222556 ROS, RNS production in phagocytes
R-HSA-9006934 Signaling by Receptor Tyrosine Kinases
R-HSA-168249 Innate Immune System
R-HSA-162582 Signal Transduction
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: NM_152565, NP_689778, Q8N8Y2, VA0D2_HUMAN
UCSC ID: uc003ydp.1
RefSeq Accession: NM_152565
Protein: Q8N8Y2 (aka VA0D2_HUMAN)
CCDS: CCDS6241.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_152565.1
exon count: 8CDS single in 3' UTR: no RNA size: 2370
ORF size: 1053CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2206.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.