Human Gene ATP6V0B (uc001cle.3)
  Description: Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b (ATP6V0B), transcript variant 2, mRNA.
RefSeq Summary (NM_001039457): This gene encodes a portion of the V0 domain of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of eukaryotic intracellular organelles. Activity of this enzyme is necessary for such varied processes as protein sorting, zymogen activation, receptor-mediated endocytosis, and synaptic vesicle proton gradient generation. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jun 2014].
Transcript (Including UTRs)
   Position: hg19 chr1:44,440,602-44,443,972 Size: 3,371 Total Exon Count: 7 Strand: +
Coding Region
   Position: hg19 chr1:44,441,787-44,443,679 Size: 1,893 Coding Exon Count: 6 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr1:44,440,602-44,443,972)mRNA (may differ from genome)Protein (158 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCLynxMalacardsMGI
neXtProtOMIMPubMedReactomeUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VATO_HUMAN
DESCRIPTION: RecName: Full=V-type proton ATPase 21 kDa proteolipid subunit; Short=V-ATPase 21 kDa proteolipid subunit; AltName: Full=Vacuolar proton pump 21 kDa proteolipid subunit; AltName: Full=hATPL;
FUNCTION: Proton-conducting pore forming subunit of the membrane integral V0 complex of vacuolar ATPase. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
SUBUNIT: Interacts with IFITM3 (By similarity).
SUBCELLULAR LOCATION: Vacuole membrane; Multi-pass membrane protein.
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the V-ATPase proteolipid subunit family.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ATP6V0B
Diseases sorted by gene-association score: lymphocytic choriomeningitis (6)

-  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: 98.57 RPKM in Whole Blood
Total median expression: 1740.88 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 -96.60203-0.476 Picture PostScript Text
3' UTR -107.82293-0.368 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
IPR002379 - ATPase_F0/V0-cplx_csu
IPR000245 - ATPase_V0-cplx_csu

Pfam Domains:
PF00137 - ATP synthase subunit C

SCOP Domains:
81333 - F1F0 ATP synthase subunit C

ModBase Predicted Comparative 3D Structure on Q99437
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:0005215 transporter activity
GO:0015078 hydrogen ion transmembrane transporter activity
GO:0046961 proton-transporting ATPase activity, rotational mechanism

Biological Process:
GO:0006811 ion 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
GO:1902600 hydrogen ion transmembrane transport

Cellular Component:
GO:0000220 vacuolar proton-transporting V-type ATPase, V0 domain
GO:0005773 vacuole
GO:0005774 vacuolar membrane
GO:0010008 endosome membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0030670 phagocytic vesicle membrane
GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain
GO:0033179 proton-transporting V-type ATPase, V0 domain


-  Descriptions from all associated GenBank mRNAs
  LF206579 - JP 2014500723-A/14082: Polycomb-Associated Non-Coding RNAs.
D89052 - Homo sapiens mRNA for proton-ATPase-like protein, complete cds.
BD062195 - Gene diagnostic agent/gene therapeutic agent of tumor using tumor specific antigen and novel application of proton pump inhibitor as antitumor drug.
JD021099 - Sequence 2123 from Patent EP1572962.
JD021596 - Sequence 2620 from Patent EP1572962.
JD021597 - Sequence 2621 from Patent EP1572962.
BC053601 - Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b, mRNA (cDNA clone IMAGE:5767662), with apparent retained intron.
BC042664 - Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b, mRNA (cDNA clone IMAGE:5180100), with apparent retained intron.
BC000423 - Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b, mRNA (cDNA clone MGC:8673 IMAGE:2964510), complete cds.
BC005876 - Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit b, mRNA (cDNA clone MGC:4498 IMAGE:2964510), complete cds.
JD029738 - Sequence 10762 from Patent EP1572962.
LF356331 - JP 2014500723-A/163834: Polycomb-Associated Non-Coding RNAs.
KJ890744 - Synthetic construct Homo sapiens clone ccsbBroadEn_00138 ATP6V0B gene, encodes complete protein.
CR456972 - Homo sapiens full open reading frame cDNA clone RZPDo834C025D for gene ATP6V0B, ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c''; complete cds, incl. stopcodon.
BT007151 - Homo sapiens ATPase, H+ transporting, lysosomal 21kDa, V0 subunit c'' mRNA, complete cds.
JD019798 - Sequence 822 from Patent EP1572962.
JD035825 - Sequence 16849 from Patent EP1572962.
HV451371 - WO 2000020442-A/2: Tumor specific antigen peptide.
LF206577 - JP 2014500723-A/14080: Polycomb-Associated Non-Coding RNAs.
JD020924 - Sequence 1948 from Patent EP1572962.
JD036308 - Sequence 17332 from Patent EP1572962.
JD022999 - Sequence 4023 from Patent EP1572962.
JD023000 - Sequence 4024 from Patent EP1572962.
JD029807 - Sequence 10831 from Patent EP1572962.
JD035824 - Sequence 16848 from Patent EP1572962.
LF356327 - JP 2014500723-A/163830: Polycomb-Associated Non-Coding RNAs.
L05089 - Homo sapiens ATPase homolog mRNA, partial cds.
JD490437 - Sequence 471461 from Patent EP1572962.
JD210846 - Sequence 191870 from Patent EP1572962.
JD392618 - Sequence 373642 from Patent EP1572962.
JD200593 - Sequence 181617 from Patent EP1572962.
JD081435 - Sequence 62459 from Patent EP1572962.
JD424077 - Sequence 405101 from Patent EP1572962.
JD424078 - Sequence 405102 from Patent EP1572962.
JD174346 - Sequence 155370 from Patent EP1572962.
JD338805 - Sequence 319829 from Patent EP1572962.
JD427710 - Sequence 408734 from Patent EP1572962.
JD124444 - Sequence 105468 from Patent EP1572962.
JD123357 - Sequence 104381 from Patent EP1572962.
JD095106 - Sequence 76130 from Patent EP1572962.
LF356324 - JP 2014500723-A/163827: Polycomb-Associated Non-Coding RNAs.
MA442156 - JP 2018138019-A/14082: Polycomb-Associated Non-Coding RNAs.
MA591908 - JP 2018138019-A/163834: Polycomb-Associated Non-Coding RNAs.
MA442154 - JP 2018138019-A/14080: Polycomb-Associated Non-Coding RNAs.
MA591904 - JP 2018138019-A/163830: Polycomb-Associated Non-Coding RNAs.
MA591901 - JP 2018138019-A/163827: Polycomb-Associated Non-Coding RNAs.

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

Reactome (by CSHL, EBI, and GO)

Protein Q99437 (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: ATP6F, NM_001039457, NP_001034546, Q6IB32, Q99437, VATO_HUMAN
UCSC ID: uc001cle.3
RefSeq Accession: NM_001039457
Protein: Q99437 (aka VATO_HUMAN)
CCDS: CCDS41315.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001039457.1
exon count: 7CDS single in 3' UTR: no RNA size: 979
ORF size: 477CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 979.00frame shift in genome: no % Coverage: 99.39
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.