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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)
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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   

Export aliases for VNN3 gene to outside databases

Previous GC identifers: GC06M132667 GC06M132891 GC06M132979 GC06M133026 GC06M133027 GC06M133085 GC06M130618


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence:
NC_000006.12  NC_018917.2  NT_025741.16  
Regulatory elements:
   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 Chromatin IP Primers for VNN3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, 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., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: VNN3_HUMAN, Q9NY84 (See protein sequence)
Recommended Name: Vascular non-inflammatory molecule 3 precursor  
Size: 501 amino acids; 56118 Da
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

Post-translational modifications: 

  • Glycosylation2 at Asn39, Asn147, Asn270, Asn358
  • 3 DME Specific Peptides for VNN3 (Q9NY84)
     YALGAFDG  YLEDIPDP  QGAHIIVTPED 


    See VNN3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB


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

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    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    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 carbon-nitrogen hydrolase superfamily. BTD/VNN family
    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,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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:    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


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    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    VNN3_HUMAN, Q9NY84: Cell membrane; Lipid-anchor, GPI-anchor (Potential). Note=According to PubMed:11491533,
    secreted (By similarity)
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    plasma membrane5
    extracellular2
    endoplasmic reticulum1
    lysosome1

    Gene Ontology (GO): 4 cellular component terms:    About this table

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

    VNN3 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to 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 QIAGEN, 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 Apr 2014 via Entrez Gene).
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        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for VNN3
    Interactions:

        Search GeneGlobe Interaction Network for VNN3

    Gene Ontology (GO): 3 biological process terms:    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, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for 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,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    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:

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

    GeneLoc Exon Structure

    Selected 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™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
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    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
     selected tissues (see all 2) fully expand
     
     Liver (Hepatobiliary System)
             Periportal Hepatocytes Liver Lobule
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
    VNN3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    VNN3 Protein Expression

    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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    (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)
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    This gene was present in the common ancestor of animals.

    Orthologs for VNN3 gene from Selected 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
    --
    Uncharacterized protein
    28(a)
    27(a)
    many ↔ many
    many ↔ many
    3(56091510-56098068)
    3(56080843-56088624)
    lizard
    (Anolis carolinensis)
    Reptilia --
    --
    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)
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    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), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for VNN3 (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: --
    Site Specific Mutation Identification with 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.)
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    OMIM gene information: 606592    OMIM disorders: --

    8 diseases for VNN3:    About MalaCards
    irritant dermatitis    contact dermatitis    allergic contact dermatitis    dermatitis
    atopic dermatitis    epididymitis    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)
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    PubMed articles for VNN3 gene integrated from 10 sources:
    (articles sorted by number of sources associating them with VNN3)
        Utopia: connect your pdf to the dynamic
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    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. (J. Invest. Dermatol. 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. (Immunogenetics 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. (Immunogenetics 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. (Gene 2008)
    5. Pharmacologic concentrations of ascorbic acid cause diverse influence on differential expressions of angiogenic chemokine genes in different hepatocellular carcinoma cell lines. (PubMed id 19932582)1, 3 Lin Z.Y. and Chuang W.L. (amp 2010)
    6. The DNA sequence and analysis of human chromosome 6. (PubMed id 14574404)1, 2 Mungall A.J.... Beck S. (Nature 2003)
    7. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. (PubMed id 16344560)1 Kimura K.... Sugano S. (Genome Res. 2006)
    8. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    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. (Proc. Natl. Acad. Sci. U.S.A. 2002)
    10. Molecular diagnostics of psoriasis, atopic dermatitis, allergic contact dermatitis and irritant contact dermatitis. (PubMed id 19818069)9 Kamsteeg M....Schalkwijk J. (Br. J. Dermatol. 2010)

    (in PubMed, OMIM, and NCBI Bookshelf)
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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, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
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    NameDescription
    PharmGKB entry for VNN3 Pharmacogenomics, SNPs, Pathways
    NIEHS-SNPshttp://egp.gs.washington.edu/data/vnn3/

    (Patent information from GeneIP,
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    IP news from LifeMap Sciences, Inc.)
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    Patent Information for VNN3 gene:
    Search GeneIP for patents involving VNN3

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



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