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Category   Symbol Source: HGNC EntrezGene Ensembl GeneCards RNA genes CroW21
GIFtS

VNN3 Gene

protein-coding   GIFtS: 45
GCID: GC06M133046

Vanin 3

  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
About This Section

This gene clusters with an RNA gene
Subcategory (RNA class): lncRNA

Quality score for the ORGUL clustered with this gene is 3

Aliases
Vanin 31 2
EC 3.5.1.923 8
HSA2389822
Vanin-33
EC 3.5.18

External Ids:    HGNC: 164311   Entrez Gene: 553502   Ensembl: ENSG000000931347   OMIM: 6065925   UniProtKB: Q9NY843   
ORGUL members:         
NONCODE14:n408167      

Export aliases for VNN3 gene to outside databases

Previous GC identifers: GC06M132667 GC06M132891 GC06M132979 GC06M133026 GC06M133027 GC06M133085 GC06M130618


(According to Entrez Gene, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
About This Section

Entrez Gene summary for VNN3 Gene:
This gene is the central gene in a cluster of three vanin genes on chromosome 6q23-q24. The open reading frame is
disrupted by a frameshift, and all splice variants that have been described are candidates for nonsense-mediated
decay (NMD). Consequently, it is unlikely that this gene expresses a protein in vivo, so it is classified as a
pseudogene. Extensive alternative splicing has been described; the two most common variants are represented as
RefSeqs. (provided by RefSeq, Aug 2009)

GeneCards Summary for VNN3 Gene: 
VNN3 (vanin 3) is a protein-coding gene, and is affiliated with the lncRNA class. Diseases associated with VNN3 include irritant dermatitis, and contact dermatitis. GO annotations related to this gene include pantetheine hydrolase activity. An important paralog of this gene is VNN1.

UniProtKB/Swiss-Prot: VNN3_HUMAN, Q9NY84
Function: Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus
recycling pantothenic acid (vitamin B5) and releasing cysteamine




(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 73), Regulatory elements and Epigenetics data according to QIAGEN, SABiosciences, and/or SwitchGear Genomics)
About This Section
RefSeq DNA sequence:
NC_000006.11  NC_018917.2  NT_025741.15  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the VNN3 gene promoter:
         USF1   RREB-1   E47   GATA-1   PPAR-gamma1   USF-1   STAT3   Hand1   PPAR-gamma2   Ik-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidVNN3 promoter sequence
   Search SABiosciences Chromatin IP Primers for VNN3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat VNN3


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 6q23.2   Ensembl cytogenetic band:  6q23.2   HGNC cytogenetic band: 6q23.2

VNN3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
VNN3 gene location

GeneLoc information about chromosome 6         GeneLoc Exon Structure

GeneLoc location for GC06M133046:  view genomic region     (about GC identifiers)

Start:
133,043,926 bp from pter      End:
133,055,904 bp from pter
Size:
11,979 bases      Orientation:
minus strand

(According to UniProtKB, HORDE, neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MAXQB RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Ontologies according to Gene Ontology Consortium 01 Oct 2013 and Entrez Gene, Antibodies by EMD Millipore, R&D Systems, GenScript, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
About This Section

UniProtKB/Swiss-Prot: VNN3_HUMAN, Q9NY84 (See protein sequence)
Recommended Name: Vascular non-inflammatory molecule 3 precursor  
Size: 501 amino acids; 56118 Da
Subcellular location: Cell membrane; Lipid-anchor, GPI-anchor (Potential). Note=According to PubMed:11491533,
secreted (By similarity)
Secondary accessions: B2DFY0 B2DFY1 B2DFY3 B2DFY5 B2DFY6 B2DFY7 B2DFY8 Q3SX90 Q9BQY2
Alternative splicing: 8 isoforms:  Q9NY84-1   Q9NY84-2   Q9NY84-3   Q9NY84-4   Q9NY84-5   Q9NY84-6   Q9NY84-7   Q9NY84-8   
(Expressed in neutrophils, this isoform displays a frameshift at Glu-227 due to one missing nucleotide compared to isoform 1, this missing nucleotide could be a variation as it is also present on genomic sequence)

Explore the universe of human proteins at neXtProt for VNN3: NX_Q9NY84

Explore proteomics data for VNN3 at MOPED 

3 DME Specific Peptides for VNN3 (Q9NY84)
 YALGAFDG  YLEDIPDP  QGAHIIVTPED 

VNN3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

VNN3 Protein Expression

ENSEMBL proteins: 
 ENSP00000438024   ENSP00000439449   ENSP00000464241   ENSP00000463583   ENSP00000444505  
 ENSP00000443901   ENSP00000444491   ENSP00000443073   ENSP00000438175   ENSP00000441182  
 ENSP00000440245   ENSP00000439815   ENSP00000440594   ENSP00000445925  

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Cloud-Clone Corp. Proteins for VNN3 

Gene Ontology (GO): 4 cellular component terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005575cellular_component ND--
GO:0005615extracellular space IEA--
GO:0005886plasma membrane IEA--
GO:0031225anchored to membrane IEA--

VNN3 for ontologies           About GeneDecksing



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Cloud-Clone Corp. CLIAs for VNN3


(According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
About This Section
HGNC Gene Families: 
VNN: Vanins

2 InterPro protein domains:
 IPR003010 C-N_Hydrolase
 IPR012101 Biotinidase_euk

Graphical View of Domain Structure for InterPro Entry Q9NY84

ProtoNet protein and cluster: Q9NY84

1 Blocks protein domain: IPB003010 Nitrilase/cyanide hydratase and apolipoprotein N-acyltransferase

UniProtKB/Swiss-Prot: VNN3_HUMAN, Q9NY84
Similarity: Belongs to the CN hydrolase family. BTD/VNN subfamily
Similarity: Contains 1 CN hydrolase domain


VNN3 for domains           About GeneDecksing


(According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
bound targets from SABiosciences, miRNA Gene Targets from miRTarBase, shRNA from OriGene, RNAi from EMD Millipore, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, Gene Editing from DNA2.0, Sirion Biotech, Clones from EMD Millipore, OriGene, SwitchGear Genomics, GenScript, Sino Biological, DNA2.0, Vector BioLabs, and Sirion Biotech, Cell Lines from GenScript, LifeMap BioReagents, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene.)
About This Section

Molecular Function:

     UniProtKB/Swiss-Prot Summary: VNN3_HUMAN, Q9NY84
Function: Amidohydrolase that hydrolyzes specifically one of the carboamide linkages in D-pantetheine thus
recycling pantothenic acid (vitamin B5) and releasing cysteamine
Catalytic activity: (R)-pantetheine + H(2)O = (R)-pantothenate + 2-aminoethanethiol
Induction: By Th17/Th1 type cytokines, but not by Th2-type

     Enzyme Numbers (IUBMB): EC 3.5.1.921 2 EC 3.5.12

     Gene Ontology (GO): 3 molecular function terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0016810hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds ----
GO:0016811hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides ----
GO:0017159pantetheine hydrolase activity NAS11491533
     
VNN3 for ontologies           About GeneDecksing


Animal Models:
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miRNA
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(Pathways according to EMD Millipore, R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to SABiosciences, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Oct 2013 via Entrez Gene).
About This Section



Interactions:

    Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for VNN3

Gene Ontology (GO): 3 biological process terms (GO ID links to tree view):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006807nitrogen compound metabolic process ----
GO:0008150biological_process ND--
GO:0015939pantothenate metabolic process IEA--

VNN3 for ontologies           About GeneDecksing



(Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB, with drugs/clinical trials/news search links to CenterWatch)
About This Section
Browse Small Molecules at EMD Millipore
Browse drugs & compounds from Enzo Life Sciences

Browse Tocris compounds for VNN3

Search CenterWatch for drugs/clinical trials and news about VNN3

(Secondary structures according to fRNAdb,
GenBank/EMBL/DDBJ Accessions according to
Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
RefSeq according to Entrez Gene,
DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
RNAi Products from EMD Millipore,
siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN,
Tagged/untagged cDNA clones from OriGene, SwitchGear Genomics, GenScript, DNA2.0, Vector BioLabs, Sirion Biotech, Primers from OriGene, SABiosciences, and/or QIAGEN )
About This Section

REFSEQ mRNAs for VNN3 gene (2 alternative transcripts): 
NM_018399.3  NM_078625.2  

Unigene Cluster for VNN3:

Vanin 3
Hs.183656  [show with all ESTs]
Unigene Representative Sequence: NR_028290
16 Ensembl transcripts including schematic representations, and UCSC links where relevant:
ENST00000367927(uc010kfs.3 uc011ecl.2 uc010kfv.3 uc010kfw.3 uc010kfx.3)
ENST00000425515(uc011ecm.2 uc010kfu.3 uc010kfy.3) ENST00000509351(uc010kfz.3)
ENST00000417437 ENST00000414302 ENST00000423615 ENST00000427187 ENST00000275223
ENST00000519686 ENST00000392393(uc011ecn.2) ENST00000450865 ENST00000544102
ENST00000580813 ENST00000448644 ENST00000207771 ENST00000392394
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Additional mRNA sequence: 

AB435052.1 AB435053.1 AB435054.1 AB435055.1 AB435056.1 AB435057.1 AB435058.1 AB435059.1 
AB435060.1 AB435061.1 AJ238982.1 AK075110.1 AK314708.1 BC104416.2 BC104417.1 BC113022.1 
BC113023.1 BC148317.2 NR_028290.1 NR_028291.1 

5 DOTS entries:

DT.91857071  DT.310281  DT.99974429  DT.100679248  DT.310282 

22 AceView cDNA sequences:

AK075110 NM_078625 BQ072901 R88731 BX099428 BX448862 AJ238982 NM_018399 
AW150782 AA461448 AA461622 R90987 R93899 T95504 T95503 BG194799 
BG190840 H59891 CD707557 BG219375 H59890 BG215781 

GeneLoc Exon Structure

5/6 Alternative Splicing Database (ASD) splice patterns (SP) for VNN3 (see all 6)    About this scheme

ExUns: 1a · 1b · 1c ^ 2a · 2b · 2c ^ 3 ^ 4a · 4b ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8
SP1:                          -     -     -                                                   
SP2:                          -     -     -     -                                             
SP3:                          -     -     -     -     -     -                                 
SP4:                          -     -                                                         
SP5:                                                                                          


ECgene alternative splicing isoforms for VNN3

(RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, plus additional links to Genevestigator, and/or SOURCE, and/or BioGPS, and/or UniProtKB,
PCR Arrays from SABiosciences, Primers from OriGene, SABiosciences, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
About This Section

VNN3 expression in normal human tissues (normalized intensities)      VNN3 embryonic expression: see
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: --
VNN3 Expression
About this image


VNN3 expression in embryonic tissues and stem cells    About this table
Data from LifeMap, the Embryonic Development and Stem Cells Database 
 5/5 selected tissues (see all 5) fully expand
 
 Blood (Hematopoietic System)    fully expand to see all 2 entries
         neutrophils   
 
 Epithelium (Respiratory System)    fully expand to see all 2 entries
         bronchial epithelial cells   
 
 Liver (Hepatobiliary System)
         Periportal Hepatocytes Liver Lobule
 
 Lung (Respiratory System)
         trachea   
 
 Adipose (Muscoskeletal System)
         epididymal fat pads   

See VNN3 Protein Expression from SPIRE MOPED and PaxDB
Genevestigator expression for VNN3

SOURCE GeneReport for Unigene cluster: Hs.183656

UniProtKB/Swiss-Prot: VNN3_HUMAN, Q9NY84
Tissue specificity: Widely expressed with higher expression in liver and blood. Expressed in differentiated
keratinocytes in epidermis and in epithelial cells in dermis. Overexpressed in lesional psoriatic skin

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In Situ
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(Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
About This Section

This gene was present in the common ancestor of animals.

Orthologs for VNN3 gene from 4/7 species (see all 7)    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
mouse
(Mus musculus)
Mammalia Vnn35 vanin 3   --   10 (11.24 cM) 23851462 
chicken
(Gallus gallus)
Aves VNN16
--
--
28(a)
27(a)
many ↔ many
many ↔ many
3(56091510-56098068)
3(56080843-56088624)
lizard
(Anolis carolinensis)
Reptilia --
Uncharacterized protein
26(a)
1 → many
GL343200.1(4437940-4448295)
fruit fly
(Drosophila melanogaster)
Insecta vanin-like3 pantetheinase 29(a)   5E1   --


ENSEMBL Gene Tree for VNN3 (if available)
TreeFam Gene Tree for VNN3 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
About This Section
Paralogs for VNN3 gene
VNN12  BTD2  VNN22  
3 SIMAP similar genes for VNN3 using alignment to 7 protein entries:     VNN3_HUMAN (see all proteins):
VNN2    VNN1    BTD

VNN3 for paralogs           About GeneDecksing



(SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD) and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers from QIAGEN, Cancer Mutation PCR Arrays and Assays and Copy Number PCR Arrays from SABiosciences)
About This Section

10/406 SNPs in VNN3 are shown (see all 406)    About this table     
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 6 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs455959451,2
C,F--133043579(-) AGACGG/TTCCTC 2 -- int18Minor allele frequency- T:0.04NS WA CSA 294
rs65698311,2
C,F,A--133043595(+) actcaG/Ctccac 2 -- int16Minor allele frequency- C:0.10NS WA 292
rs455309341,2
C,F--133043603(-) TTGAAT/CTGGTG 2 -- int17Minor allele frequency- C:0.06NS WA EA 412
rs1853966521,2
--133043609(+) TTCAAA/GTGCTG 2 -- int10--------
rs456108411,2
C,F--133043682(-) GTCATG/AAGATG 2 -- int16Minor allele frequency- A:0.01NS NA 292
rs454427931,2
C,F--133043711(-) TGGTTA/CATTTT 2 -- int17Minor allele frequency- C:0.06NS WA 294
rs1906891911,2
--133043732(+) GAAACA/TACACT 2 -- int10--------
rs69070201,2
C,F,A,H--133043800(+) ATATAC/TGCTCC 2 -- int120Minor allele frequency- T:0.15NS EA NA CSA WA 1849
rs1928429631,2
--133043892(+) TACCAA/GACATG 2 -- int10--------
rs1386504161,2
--133043923(+) CACACC/TTGTTG 2 -- int10--------

HapMap Linkage Disequilibrium report for VNN3 (133043926 - 133055904 bp)

Structural Variations
      Database of Genomic Variants (DGV) variations for VNN3: --
SABiosciences Cancer Mutation PCR Assays
Search QIAGEN SeqTarget long-range PCR primers for resequencing VNN3
DNA2.0 Custom Variant and Variant Library Synthesis for VNN3

(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
About This Section
OMIM gene information: 606592    OMIM disorders: --

7 diseases for VNN3:    About MalaCards
irritant dermatitis    contact dermatitis    allergic contact dermatitis    dermatitis
atopic dermatitis    psoriasis    hepatocellular carcinoma


VNN3 for disorders           About GeneDecksing


Export disorders for VNN3 gene to outside databases

(in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
About This Section

PubMed articles for VNN3 gene integrated from 9 sources:
(articles sorted by number of sources associating them with VNN3)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Expression of the vanin gene family in normal and inflamed human skin: induction by proinflammatory cytokines. (PubMed id 19322213)1, 2, 3, 9 Jansen P.A.M.... Schalkwijk J. (2009)
  2. An ESTs description of the new vanin gene family conserved from fly to human. (PubMed id 10501839)1, 2, 3 Granjeaud S.... Galland F. (1999)
  3. Vanin genes are clustered (human 6q22-24 and mouse 10A2B1) and encode isoforms of pantetheinase ectoenzymes. (PubMed id 11491533)1, 2, 9 Martin F....Galland F. (2001)
  4. Alternative spliced variants in the pantetheinase family of genes expressed in human neutrophils. (PubMed id 18805469)1, 2, 9 Nitto T.... Node K. (2008)
  5. Pharmacologic concentrations of ascorbic acid cause d iverse influence on differential expressions of angiogenic chemokine genes in d ifferent hepatocellular carcinoma cell lines. (PubMed id 19932582)1, 3 Lin Z.Y. and Chuang W.L. (2010)
  6. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (2003)
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  9. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. (PubMed id 12477932)1 Strausberg R.L....Marra M.A. (2002)
  10. Molecular diagnostics of psoriasis, atopic dermatitis , allergic contact dermatitis and irritant contact dermatitis. (PubMed id 19818069)9 Kamsteeg M....Schalkwijk J. (2010)

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(According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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Entrez Gene: 55350 HGNC: 16431 AceView: VNN3 Ensembl:ENSG00000093134 euGenes: HUgn55350
ECgene: VNN3 H-InvDB: VNN3

(According to HUGE)
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  --

(According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
Wikipedia and/or GeneReviews via UniProtKB/Swiss-Prot)
About This Section
NameDescription
PharmGKB entry for VNN3 Pharmacogenomics, SNPs, Pathways
NIEHS-SNPshttp://egp.gs.washington.edu/data/vnn3/

(Patent information from GeneIP,
Licensable technologies from WIS Yeda, Salk, Tufts,
IP news from LifeMap Sciences, Inc.)
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Patent Information for VNN3 gene:
Search GeneIP for patents involving VNN3

GeneCards and IP:
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