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

DEFA3 Gene

protein-coding   GIFtS: 56
GCID: GC08M006875

Defensin, Alpha 3, Neutrophil-Specific


(Previous symbol: DEF3)
Microbiology & Infectious Diseases Congress
  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

Aliases
Defensin, Alpha 3, Neutrophil-Specific1 2     HNP32
DEF31 2 3     Defensin 3, Neutrophil-Specific2
HNP-32 3     Neutrophil Defensin 32
HP-32 3     Neutrophil Peptide 32
HP32 3     Defensin, Alpha 33

External Ids:    HGNC: 27621   Entrez Gene: 16682   Ensembl: ENSG000002398397   OMIM: 6045225   UniProtKB: P596663   

Export aliases for DEFA3 gene to outside databases

Previous GC identifers: GC08M006918 GC08M007108 GC08M007033 GC08M006860


(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 DEFA3 Gene:
Defensins are a family of microbicidal and cytotoxic peptides thought to be involved in host defense. They are
abundant in the granules of neutrophils and also found in the epithelia of mucosal surfaces such as those of the
intestine, respiratory tract, urinary tract, and vagina. Members of the defensin family are highly similar in
protein sequence and distinguished by a conserved cysteine motif. The protein encoded by this gene, defensin,
alpha 3, is found in the microbicidal granules of neutrophils and likely plays a role in phagocyte-mediated host
defense. Several alpha defensin genes are clustered on chromosome 8. This gene differs from defensin, alpha 1 by
only one amino acid. This gene and the gene encoding defensin, alpha 1 are both subject to copy number variation.
(provided by RefSeq, May 2010)

GeneCards Summary for DEFA3 Gene: 
DEFA3 (defensin, alpha 3, neutrophil-specific) is a protein-coding gene. Diseases associated with DEFA3 include ramsay-hunt syndrome, and chronic myelomonocytic leukemia, and among its related super-pathways are Immune System and Beta defensins. An important paralog of this gene is DEFA1B.

UniProtKB/Swiss-Prot: DEF3_HUMAN, P59666
Function: Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial
activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by
permeabilizing their plasma membrane

Gene Wiki entry for DEFA3 Gene


(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_000008.10  NC_018919.2  NT_023736.17  
Regulatory elements:
   SABiosciences Regulatory transcription factor binding sites in the DEFA3 gene promoter:
         AML1a   c-Myb   Nkx2-5   FOXL1   
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search SABiosciences Chromatin IP Primers for DEFA3

Epigenetics:
QIAGEN PyroMark CpG Assay predesigned Pyrosequencing DNA Methylation assays in human, mouse, rat DEFA3


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

Entrez Gene cytogenetic band: 8p23.1   Ensembl cytogenetic band:  8p23.1   HGNC cytogenetic band: 8p23.1

DEFA3 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFA3 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M006875:  view genomic region     (about GC identifiers)

Start:
6,873,391 bp from pter      End:
6,875,823 bp from pter
Size:
2,433 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: DEF3_HUMAN, P59666 (See protein sequence)
Recommended Name: Neutrophil defensin 3 precursor  
Size: 94 amino acids; 10245 Da
Subunit: Dimer
Subcellular location: Secreted
6 PDB 3D structures from and Proteopedia for DEFA3:
1DFN (3D)        1ZMH (3D)        1ZMI (3D)        1ZMK (3D)        2PM4 (3D)        2PM5 (3D)    
Secondary accessions: P11479 Q14125

Explore the universe of human proteins at neXtProt for DEFA3: NX_P59666

Explore proteomics data for DEFA3 at MOPED 

Post-translational modifications:

  • View modification sites using PhosphoSitePlus
  • View neXtProt modification sites for NX_P59666

  • DEFA3 Protein expression data from MOPED1, PaxDb2 and MAXQB3 :    About this image 

    DEFA3 Protein Expression
    REFSEQ proteins: NP_005208.1  
    ENSEMBL proteins: 
     ENSP00000328359  
    Reactome Protein details: P59666
    Human Recombinant Protein Products for DEFA3: 
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    Browse Sino Biological Cell Lysates 
    Browse ProSpec Recombinant Proteins
    Browse Proteins at Cloud-Clone Corp. 

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

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005615extracellular space IEA--
    GO:0005796Golgi lumen TAS--
    GO:0035578azurophil granule lumen TAS--

    DEFA3 for ontologies           About GeneDecksing



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

    4 InterPro protein domains:
     IPR016327 Alpha-defensin
     IPR006080 Defensin_beta/neutrophil
     IPR006081 Mammalian_defensins
     IPR002366 Defensin_propep

    Graphical View of Domain Structure for InterPro Entry P59666

    ProtoNet protein and cluster: P59666

    1 Blocks protein domain: IPB002366 Defensin propeptide

    UniProtKB/Swiss-Prot: DEF3_HUMAN, P59666
    Similarity: Belongs to the alpha-defensin family


    DEFA3 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: DEF3_HUMAN, P59666
    Function: Defensin 2 and defensin 3 have antibiotic, fungicide and antiviral activities. Has antimicrobial
    activity against Gram-negative and Gram-positive bacteria. Defensins are thought to kill microbes by
    permeabilizing their plasma membrane

         Genatlas biochemistry entry for DEFA3:
    defensin alpha 3,3-4kDa,,hematopoietic,released from azurophil granules of neutrophiles,oxygen independent
    phagocytosis of Gram+,Gram- bacteria,many fungi,some viruses

    Phenotypes:
         1 GenomeRNAi human phenotype for DEFA3:
     Increased gamma-H2AX phosphory 

    Animal Models:
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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

    SuperPaths for DEFA3 About                                                                                                See pathways by source

    SuperPathContained pathways About
    1Immune System
    Immune System0.56
    Innate Immune System0.50
    2Beta defensins
    Defensins0.80
    3Transcriptional misregulation in cancer
    Transcriptional misregulation in cancer
    4Alpha-defensins
    Alpha-defensins
    5Selected targets of C/EBPalpha
    Selected targets of C/EBPalpha

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways

    1 EMD Millipore Pathway for DEFA3
        Selected targets of C/EBPalpha



    4        Reactome Pathways for DEFA3
        Defensins
    Alpha-defensins
    Immune System
    Innate Immune System


    1         Kegg Pathway  (Kegg details for DEFA3):
        Transcriptional misregulation in cancer


    DEFA3 for pathways           About GeneDecksing

    Interactions:

        Search SABiosciences Gene Network CentralTM Interacting Genes and Proteins Networks for DEFA3

    STRING Interaction Network Preview (showing 1 interactants - click image to see more details)

    3 Interacting proteins for DEFA3 (P596662, 3 ENSP000003283594) via UniProtKB, MINT, STRING, and/or I2D
    InteractantInteraction Details
    GeneCardExternal ID(s)
    PFDN1O609252, 3MINT-63191 I2D: score=1 
    DEFA1P596653, ENSP000003721264I2D: score=1 STRING: ENSP00000372126
    DEFA1BP596653I2D: score=1 
    About this table

    Gene Ontology (GO): 5/6 biological process terms (GO ID links to tree view) (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006952defense response ----
    GO:0031640killing of cells of other organism IEA--
    GO:0042742defense response to bacterium IEA--
    GO:0045087innate immune response TAS--
    GO:0050832defense response to fungus IEA--

    DEFA3 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

    DEFA3 for compounds           About GeneDecksing

    Browse Small Molecules at EMD Millipore
    Browse drugs & compounds from Enzo Life Sciences

    Browse Tocris compounds for DEFA3 (DEF3)

    3 Novoseek inferred chemical compound relationships for DEFA3 gene    About this table
    Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
    hbd2 82.2 3 12654098 (1), 20020833 (1), 10906336 (1)
    anti-fungal 11.3 1 10769165 (1)
    arginine 0.342 2 10769165 (2)

    Search CenterWatch for drugs/clinical trials and news about DEFA3 / DEF3

    (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 DEFA3 gene: 
    NM_005217.3  

    Unigene Cluster for DEFA3:

    Defensin, alpha 3, neutrophil-specific
    Hs.654448  [show with all ESTs]
    Unigene Representative Sequence: BX427053
    1 Ensembl transcript including schematic representation, and UCSC links where relevant:
    ENST00000327857(uc003wqz.1)
    Congresses - knowledge worth sharing:  
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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    Additional mRNA sequence: 

    BC027917.1 BC119706.2 M21131.1 M23281.1 X13621.1 

    2 DOTS entries:

    DT.87017167  DT.40131822 

    24/377 AceView cDNA sequences (see all 377):

    AJ705663 BE831364 BM725836 AJ706312 AW467613 BE831397 AA321199 AJ713328 
    BC069423 AW468012 BE831398 AW440905 BP429396 AA321316 BE831411 BE831403 
    BE831369 AA321190 AW236257 M21130 BE831402 BE831385 BE831404 AW274523 

    GeneLoc Exon Structure


    (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

    DEFA3 expression in normal human tissues (normalized intensities)      DEFA3 embryonic expression: see
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: GACTGCTATT
    DEFA3 Expression
    About this image


    DEFA3 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database 
     5/3 selected tissues (see all 3) fully expand
     
     Blood (Hematopoietic System)
             bone marrow   
     
     Epidermis (Integumentary System)
             Full-thickness skin substitutes
     
     Bone (Muscoskeletal System)
             bone marrow   

    See DEFA3 Protein Expression from SPIRE MOPED and PaxDB
    Genevestigator expression for DEFA3

    SOURCE GeneReport for Unigene cluster: Hs.654448
        SABiosciences Custom PCR Arrays for DEFA3
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    In Situ
    Assay Products:
     

     
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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
      --

    ENSEMBL Gene Tree for DEFA3 (if available)
    TreeFam Gene Tree for DEFA3 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
    About This Section
    Paralogs for DEFA3 gene
    DEFA1B1 2  DEFA11 2  DEFA62  DEFA42  DEFA52  
    6 SIMAP similar genes for DEFA3 using alignment to 2 protein entries:     DEF3_HUMAN (see all proteins):
    DEFA1    DEFA1B    DEFA4    DEFA5    DEFA6    Em

    DEFA3 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

    10/130 SNPs in DEFA3 are shown (see all 130)    About this table     
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs2013209371,2
    C--6872892(+) GAGGAC/TGTGCC 1 -- ds50010--------
    rs1996081761,2
    C--6872994(+) GTAACA/CCTATG 1 -- ds50010--------
    rs1421155401,2
    C--6872998(+) CCCTAC/TGTCTT 1 -- ds50010--------
    rs2010130941,2
    C--6873067(+) GATGG-/TTTTTT 1 -- ds50010--------
    rs1477867351,2
    C--6873126(+) ACCGAC/TTGTTT 1 -- ds50010--------
    rs1500087811,2
    F--6873581(+) ATGCAC/TGCTGG 2 A syn11Minor allele frequency- T:0.01NA 4102
    rs1450766811,2
    C--6873603(+) AGCAGG/TCCATG 2 D A mis10--------
    rs2001351171,2
    C--6873621(+) TTGAGC/TCTGGG 2 D G mis11Minor allele frequency- T:0.00EU 1159
    rs1482983801,2
    C--6873708(+) CTGACA/CGGTGA 1 -- int10--------
    rs1391646301,2
    C--6873725(+) CTGCAC/TTGCAG 1 -- int10--------

    HapMap Linkage Disequilibrium report for DEFA3 (6873391 - 6875823 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 10/24 variations for DEFA3 (see all 24):    About this table     
    Variant IDTypeSubtypePubMed ID
    nsv435861CNV Deletion17901297
    nsv820476CNV Duplication20802225
    nsv6064CNV Insertion18451855
    nsv890070CNV Loss21882294
    nsv437041CNV Loss16327808
    nsv6060CNV Loss18451855
    nsv831221CNV Gain17160897
    nsv528374CNV Gain19592680
    esv2752262CNV Gain17911159
    nsv482119CNV Gain20164927

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    (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: 604522    OMIM disorders: --

    20/29 diseases for DEFA3 (see all 29):    About MalaCards
    ramsay-hunt syndrome    chronic myelomonocytic leukemia    clostridium difficile    bell's palsy
    multidrug-resistant tuberculosis    pulmonary tuberculosis    chronic venous leg ulcers    bacterial vaginosis
    pterygium    vaginitis    periodontal disease    tuberculosis
    peritonitis    gingivitis    periodontitis    endometriosis
    meningioma    pulmonary fibrosis    systemic lupus erythematosus    pneumonia


    DEFA3 for disorders           About GeneDecksing

    Genetic Association Database (GAD): DEFA3
    Human Genome Epidemiology (HuGE) Navigator: DEFA3 (7 documents)

    Export disorders for DEFA3 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 DEFA3 gene, integrated from 9 sources (see all 98):
    (articles sorted by number of sources associating them with DEFA3)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. The structure of neutrophil defensin genes. (PubMed id 8477861)1, 2, 3, 9 Linzmeier R.... Ganz T. (1993)
    2. Inter-population variability of DEFA3 gene absence: correlation with haplotype structure and population variability. (PubMed id 17214878)1, 3, 9 Ballana E....Estivill X. (2007)
    3. Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3. (PubMed id 15944200)1, 3, 9 Aldred P.M....Armour J.A. (2005)
    4. Risk of meningioma and common variation in genes rela ted to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (2010)
    5. Increased genomic copy number of DEFA1/DEFA3 is assoc iated with susceptibility to severe sepsis in Chinese Han population. (PubMed id 20502117)1, 4 Chen Q....Fang X. (2010)
    6. Polymorphisms in innate immunity genes and risk of ch ildhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (2010)
    7. Copy number variation of defensin genes and HIV infection in Brazilian children. (PubMed id 19194307)1, 4 Milanese M....Crovella S. (2009)
    8. MRPS18CP2 alleles and DEFA3 absence as putative chromosome 8p23.1 modifiers of hearing loss due to mtDNA mutation A1555G in the 12S rRNA gene. (PubMed id 18154640)1, 4 Ballana E....Estivill X. (2007)
    9. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S....Malek J. (2004)
    10. The structure of neutrophil defensin genes. (PubMed id 8325384)1, 2 Linzmeier R....Ganz T. (1993)

    (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)
    About This Section
    Entrez Gene: 1668 HGNC: 2762 AceView: DEFA1andDEFA3 Ensembl:ENSG00000239839 euGenes: HUgn1668
    ECgene: DEFA3 Kegg: 1668 H-InvDB: DEFA3

    (According to HUGE)
    About This Section
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    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL,
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    About This Section
    NameDescription
    PharmGKB entry for DEFA3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
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    Patent Information for DEFA3 gene:
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