Human Gene ATP6V1C1 (uc003ykz.4) Description and Page Index
  Description: Homo sapiens ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 (ATP6V1C1), mRNA.
RefSeq Summary (NM_001695): This gene encodes a component of vacuolar ATPase (V-ATPase), a multisubunit enzyme that mediates acidification of intracellular compartments of eukaryotic cells. V-ATPase dependent 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 is one of two genes that encode the V1 domain C subunit proteins and is found ubiquitously. This C subunit is analogous but not homologous to gamma subunit of F-ATPases. Previously, this gene was designated ATP6D. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR1803614.70718.1, SRR1803612.140832.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA1966682 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000518738.2/ ENSP00000430282.1 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:104,033,248-104,085,285 Size: 52,038 Total Exon Count: 13 Strand: +
Coding Region
   Position: hg19 chr8:104,053,065-104,080,975 Size: 27,911 Coding Exon Count: 12 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsCTDGene 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 (chr8:104,033,248-104,085,285)mRNA (may differ from genome)Protein (382 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
GeneNetworkH-INVHGNCHPRDLynxMGI
neXtProtOMIMPubMedReactomeStanford SOURCETreefam
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: VATC1_HUMAN
DESCRIPTION: RecName: Full=V-type proton ATPase subunit C 1; Short=V-ATPase subunit C 1; AltName: Full=Vacuolar proton pump subunit C 1;
FUNCTION: Subunit of the peripheral V1 complex of vacuolar ATPase. Subunit C is necessary for the assembly of the catalytic sector of the enzyme and is likely to have a specific function in its catalytic activity. V-ATPase is responsible for acidifying a variety of intracellular compartments in eukaryotic cells.
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).
INTERACTION: P62330:ARF6; NbExp=4; IntAct=EBI-988663, EBI-638181;
TISSUE SPECIFICITY: Ubiquitous.
SIMILARITY: Belongs to the V-ATPase C subunit family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): ATP6V1C1
CDC HuGE Published Literature: ATP6V1C1
Positive Disease Associations: Stroke
Related Studies:
  1. Stroke
    , , . [PubMed 0]

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene
  • D013749 Tetrachlorodibenzodioxin
  • C517041 (4-amino-1,4-dihydro-3-(2-pyridyl)-5-thioxo-1,2,4-triazole)copper(II)
  • C495626 14-deoxy-11,12-didehydroandrographolide
  • C532162 2-(1H-indazol-4-yl)-6-(4-methanesulfonylpiperazin-1-ylmethyl)-4-morpholin-4-ylthieno(3,2-d)pyrimidine
  • C030370 2-methoxy-5-(2',3',4'-trimethoxyphenyl)tropone
  • D001564 Benzo(a)pyrene
  • D004390 Chlorpyrifos
  • D002945 Cisplatin
  • D003300 Copper
  • D019327 Copper Sulfate
          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: 36.88 RPKM in Brain - Frontal Cortex (BA9)
Total median expression: 619.35 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 -94.70245-0.387 Picture PostScript Text
3' UTR -1208.914310-0.280 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
IPR004907 - ATPase_V1-cplx_csu

Pfam Domains:
PF03223 - V-ATPase subunit C

ModBase Predicted Comparative 3D Structure on P21283
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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: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: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:0000221 vacuolar proton-transporting V-type ATPase, V1 domain
GO:0005737 cytoplasm
GO:0005765 lysosomal membrane
GO:0005829 cytosol
GO:0005886 plasma membrane
GO:0016469 proton-transporting two-sector ATPase complex
GO:0031410 cytoplasmic vesicle
GO:0033180 proton-transporting V-type ATPase, V1 domain
GO:0045177 apical part of cell
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  HM005536 - Homo sapiens clone HTL-T-223 testicular tissue protein Li 223 mRNA, complete cds.
AK298617 - Homo sapiens cDNA FLJ52191 complete cds, highly similar to Vacuolar ATP synthase subunit C (EC 3.6.3.14).
BX648079 - Homo sapiens mRNA; cDNA DKFZp686N08183 (from clone DKFZp686N08183).
AK308632 - Homo sapiens cDNA, FLJ98673.
BC010960 - Homo sapiens ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1, mRNA (cDNA clone MGC:13646 IMAGE:4108687), complete cds.
X69151 - H.sapiens mRNA for subunit C of vacuolar proton-ATPase V1 domain.
AK000064 - Homo sapiens cDNA FLJ20057 fis, clone COL01311, highly similar to J05682 Human subunit C of V-ATPase.
CU679864 - Synthetic construct Homo sapiens gateway clone IMAGE:100018187 5' read ATP6V1C1 mRNA.
KJ890742 - Synthetic construct Homo sapiens clone ccsbBroadEn_00136 ATP6V1C1 gene, encodes complete protein.
AB587440 - Synthetic construct DNA, clone: pF1KB7276, Homo sapiens ATP6V1C1 gene for ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1, without stop codon, in Flexi system.
EU832431 - Synthetic construct Homo sapiens clone HAIB:100067460; DKFZo004G1228 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 protein (ATP6V1C1) gene, encodes complete protein.
HQ447211 - Synthetic construct Homo sapiens clone IMAGE:100070510; CCSB006365_01 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 (ATP6V1C1) gene, encodes complete protein.
EU832346 - Synthetic construct Homo sapiens clone HAIB:100067375; DKFZo008G1227 ATPase, H+ transporting, lysosomal 42kDa, V1 subunit C1 protein (ATP6V1C1) gene, encodes complete protein.
J05682 - Human subunit C of V-ATPase (vat C) mRNA, 3' end.
JD226861 - Sequence 207885 from Patent EP1572962.
JD563736 - Sequence 544760 from Patent EP1572962.
JD365346 - Sequence 346370 from Patent EP1572962.
DQ585912 - Homo sapiens piRNA piR-53024, complete sequence.
AK090702 - Homo sapiens cDNA FLJ33383 fis, clone BRACE2006514.
JD138853 - Sequence 119877 from Patent EP1572962.
JD090929 - Sequence 71953 from Patent EP1572962.

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

Reactome (by CSHL, EBI, and GO)

Protein P21283 (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: ATP6C, ATP6D, NM_001695, NP_001686, P21283, VATC, VATC1_HUMAN
UCSC ID: uc003ykz.4
RefSeq Accession: NM_001695
Protein: P21283 (aka VATC1_HUMAN)
CCDS: CCDS6296.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001695.4
exon count: 13CDS single in 3' UTR: no RNA size: 5704
ORF size: 1149CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 2486.00frame 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.