Human Gene VDAC1 (ENST00000265333.8) from GENCODE V44
  Description: Homo sapiens voltage dependent anion channel 1 (VDAC1), transcript variant 1, mRNA. (from RefSeq NM_003374)
RefSeq Summary (NM_003374): This gene encodes a voltage-dependent anion channel protein that is a major component of the outer mitochondrial membrane. The encoded protein facilitates the exchange of metabolites and ions across the outer mitochondrial membrane and may regulate mitochondrial functions. This protein also forms channels in the plasma membrane and may be involved in transmembrane electron transport. Alternate splicing results in multiple transcript variants. Multiple pseudogenes of this gene are found on chromosomes 1, 2 3, 6, 9, 12, X and Y.[provided by RefSeq, Sep 2010].
Gencode Transcript: ENST00000265333.8
Gencode Gene: ENSG00000213585.11
Transcript (Including UTRs)
   Position: hg38 chr5:133,971,871-134,004,975 Size: 33,105 Total Exon Count: 9 Strand: -
Coding Region
   Position: hg38 chr5:133,972,771-133,993,012 Size: 20,242 Coding Exon Count: 8 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
RNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther SpeciesGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2023-08-18 00:09:47

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr5:133,971,871-134,004,975)mRNA (may differ from genome)Protein (283 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGencodeGeneCards
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeUniProtKBBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: VDAC1_HUMAN
DESCRIPTION: RecName: Full=Voltage-dependent anion-selective channel protein 1; Short=VDAC-1; Short=hVDAC1; AltName: Full=Outer mitochondrial membrane protein porin 1; AltName: Full=Plasmalemmal porin; AltName: Full=Porin 31HL; AltName: Full=Porin 31HM;
FUNCTION: Forms a channel through the mitochondrial outer membrane and also the plasma membrane. The channel at the outer mitochondrial membrane allows diffusion of small hydrophilic molecules; in the plasma membrane it is involved in cell volume regulation and apoptosis. It adopts an open conformation at low or zero membrane potential and a closed conformation at potentials above 30-40 mV. The open state has a weak anion selectivity whereas the closed state is cation-selective. May participate in the formation of the permeability transition pore complex (PTPC) responsible for the release of mitochondrial products that triggers apoptosis.
SUBUNIT: Interacts with hexokinases (By similarity). Interacts with BCL2L1. Interacts with influenza A virus PB1-F2 protein.
INTERACTION: P19367:HK1; NbExp=2; IntAct=EBI-354158, EBI-713162;
SUBCELLULAR LOCATION: Mitochondrion outer membrane. Cell membrane.
TISSUE SPECIFICITY: Heart, liver and skeletal muscle.
DOMAIN: Consists mainly of a membrane-spanning beta-barrel formed by 19 beta-strands. The helical N-terminus folds back into the pore opening and plays a role in voltage-gated channel activity.
SIMILARITY: Belongs to the eukaryotic mitochondrial porin 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: VDAC1
Diseases sorted by gene-association score: cystic fibrosis (3), gerstmann-straussler disease (2), retinitis pigmentosa 14 (1)

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

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 182.82 RPKM in Muscle - Skeletal
Total median expression: 2845.82 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 -36.9087-0.424 Picture PostScript Text
3' UTR -216.00900-0.240 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
IPR001925 - Porin_Euk

Pfam Domains:
PF01459 - Eukaryotic porin

Protein Data Bank (PDB) 3-D Structure
MuPIT help
2JK4 - X-ray MuPIT 2K4T - NMR MuPIT


ModBase Predicted Comparative 3D Structure on P21796
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
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0008308 voltage-gated anion channel activity
GO:0015288 porin activity
GO:0019901 protein kinase binding
GO:0044325 ion channel binding

Biological Process:
GO:0006811 ion transport
GO:0006820 anion transport
GO:0006915 apoptotic process
GO:0015698 inorganic anion transport
GO:0016032 viral process
GO:0016236 macroautophagy
GO:0030855 epithelial cell differentiation
GO:0055085 transmembrane transport
GO:0098656 anion transmembrane transport
GO:1903146 regulation of mitophagy

Cellular Component:
GO:0005634 nucleus
GO:0005739 mitochondrion
GO:0005741 mitochondrial outer membrane
GO:0005757 mitochondrial permeability transition pore complex
GO:0005886 plasma membrane
GO:0016020 membrane
GO:0016021 integral component of membrane
GO:0042645 mitochondrial nucleoid
GO:0045121 membrane raft
GO:0046930 pore complex
GO:0070062 extracellular exosome


-  Descriptions from all associated GenBank mRNAs
  AK122953 - Homo sapiens cDNA FLJ16670 fis, clone THYMU3001133, highly similar to Voltage-dependent anion-selective channel protein 1.
BC008482 - Homo sapiens voltage-dependent anion channel 1, mRNA (cDNA clone MGC:14782 IMAGE:4332199), complete cds.
BC090042 - Homo sapiens voltage-dependent anion channel 1, mRNA (cDNA clone MGC:111064 IMAGE:30395350), complete cds.
BC071168 - Homo sapiens voltage-dependent anion channel 1, mRNA (cDNA clone MGC:88007 IMAGE:6023095), complete cds.
CS607875 - Sequence 4 from Patent WO2007043049.
HM035071 - Homo sapiens sperm binding protein 1a mRNA, complete cds.
L06132 - Human voltage-dependent anion channel isoform 1 (VDAC) mRNA, complete cds.
AK095989 - Homo sapiens cDNA FLJ38670 fis, clone HSYRA2000190, highly similar to Voltage-dependent anion-selective channel protein 1.
JD304568 - Sequence 285592 from Patent EP1572962.
JD270252 - Sequence 251276 from Patent EP1572962.
JD300984 - Sequence 282008 from Patent EP1572962.
AK293639 - Homo sapiens cDNA FLJ57715 complete cds, highly similar to Voltage-dependent anion-selective channel protein 1.
JD227421 - Sequence 208445 from Patent EP1572962.
DQ893183 - Synthetic construct clone IMAGE:100005813; FLH194827.01X; RZPDo839F0680D voltage-dependent anion channel 1 (VDAC1) gene, encodes complete protein.
KJ892370 - Synthetic construct Homo sapiens clone ccsbBroadEn_01764 VDAC1 gene, encodes complete protein.
DQ896492 - Synthetic construct Homo sapiens clone IMAGE:100010952; FLH194823.01L; RZPDo839F0670D voltage-dependent anion channel 1 (VDAC1) gene, encodes complete protein.
AB590378 - Synthetic construct DNA, clone: pFN21AE2162, Homo sapiens VDAC1 gene for voltage-dependent anion channel 1, without stop codon, in Flexi system.
JD274438 - Sequence 255462 from Patent EP1572962.
JD142956 - Sequence 123980 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa04020 - Calcium signaling pathway
hsa05012 - Parkinson's disease
hsa05016 - Huntington's disease

Reactome (by CSHL, EBI, and GO)

Protein P21796 (Reactome details) participates in the following event(s):

R-HSA-5205682 Parkin promotes the ubiquitination of mitochondrial substrates
R-HSA-5205673 p62 binds ubiquitinated mitochondrial substrates
R-HSA-1268025 SAM50 complex inserts proteins into mitochondrial outer membrane
R-HSA-5205649 p62 links damaged mitochondria to LC3
R-HSA-8949145 VDAC1,2,3 translocate calcium from the cytosol to the mitochondrial intermembrane space
R-HSA-5696872 USP30 deubiquitinates Ub-MOM proteins
R-HSA-5205663 LC3 binds the autophagosome membrane Atg5-Atg12 complex
R-HSA-5205685 Pink/Parkin Mediated Mitophagy
R-HSA-1268020 Mitochondrial protein import
R-HSA-5205647 Mitophagy
R-HSA-392499 Metabolism of proteins
R-HSA-8949215 Mitochondrial calcium ion transport
R-HSA-5689880 Ub-specific processing proteases
R-HSA-382551 Transport of small molecules
R-HSA-5688426 Deubiquitination
R-HSA-597592 Post-translational protein modification

-  Other Names for This Gene
  Alternate Gene Symbols: B3KVK4, D3DQ93, ENST00000265333.1, ENST00000265333.2, ENST00000265333.3, ENST00000265333.4, ENST00000265333.5, ENST00000265333.6, ENST00000265333.7, NM_003374, P21796, Q5FVE7, Q9UIQ5, Q9UPL0, uc003kyr.1, uc003kyr.2, uc003kyr.3, uc003kyr.4, VDAC, VDAC1_HUMAN
UCSC ID: ENST00000265333.8
RefSeq Accession: NM_003374
Protein: P21796 (aka VDAC1_HUMAN or POR1_HUMAN)
CCDS: CCDS4168.1

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