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DEFA3 Gene

protein-coding   GIFtS: 57
GCID: GC08M006875

Defensin, Alpha 3, Neutrophil-Specific


(Previous symbol: DEF3)
  See DEFA3-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
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, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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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 bell's palsy, and multidrug-resistant tuberculosis. 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 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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RefSeq DNA sequence at NCBI GenBank:
NC_000008.10  NC_018919.2  NT_023736.18  
Regulatory elements:
   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 Chromatin IP Primers for DEFA3

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing 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 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, Cloud-Clone Corp., eBioscience, and/or antibodies-online,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, Cloud-Clone Corp., eBioscience, and/or antibodies-online, Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, Abcam, Cloud-Clone Corp, antibodies-online, and/or others.)
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UniProtKB/Swiss-Prot: DEF3_HUMAN, P59666 (See protein sequence)
Recommended Name: Neutrophil defensin 3 precursor  
Size: 94 amino acids; 10245 Da
Subunit: Dimer
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: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See DEFA3 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_005208.1  
    ENSEMBL proteins: 
     ENSP00000328359  
    Reactome Protein details: P59666

    DEFA3 Human Recombinant Protein Products:

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    Browse Proteins at Cloud-Clone Corp.

     
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    antibodies-online proteins for DEFA3 (7 products) 

     
    antibodies-online peptides for DEFA3

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    antibodies-online antibodies for DEFA3 (22 products) 

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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:
    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


    Find genes that share domains with DEFA3           About GenesLikeMe


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, 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, Vector BioLabs and/or Addgene, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Flow cytometry from eBioscience, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    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

         Gene Ontology (GO): 1 molecular function term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003674molecular_function ND--
         
    Find genes that share ontologies with DEFA3           About GenesLikeMe


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

    Animal Models:
       genOway: Develop your customized and physiologically relevant rodent model for DEFA3

    miRNA
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    hsa-mir-26b-5p (MIRT028746)

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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
    DEF3_HUMAN, P59666: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    golgi apparatus4
    lysosome4
    vacuole4

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

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

    Find genes that share ontologies with DEFA3           About GenesLikeMe


    (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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    SuperPaths for DEFA3 About    
    See pathways by source

    SuperPathContained pathways About
    1Defensins
    Defensins0.80
    Alpha-defensins0.00
    2Transcriptional misregulation in cancer
    Transcriptional misregulation in cancer
    3Selected targets of C EBPalpha
    Selected targets of C EBPalpha


    Find genes that share SuperPaths with DEFA3           About GenesLikeMe

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways



    2 Reactome Pathways for DEFA3
        Defensins
    Alpha-defensins


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

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DEFA3
    Interactions:

        Search GeneGlobe Interaction Network 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): Selected biological process terms (see all 8):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006952defense response ----
    GO:0019731antibacterial humoral response IDA15616305
    GO:0030520intracellular estrogen receptor signaling pathway IDA--
    GO:0031640killing of cells of other organism IEA--
    GO:0042742defense response to bacterium ----

    Find genes that share ontologies with DEFA3           About GenesLikeMe



    (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 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)



    Find genes that share compounds with DEFA3           About GenesLikeMe



    (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,
    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, and/or Addgene, Primers from OriGene, and/or QIAGEN, Flow cytometry from eBioscience )
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    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)
    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 

    Selected AceView cDNA sequences (see all 377):

    BE831407 BE831404 AW950276 BE831402 BE831314 BE831411 AW440905 BE831405 
    AA321190 BE831369 AJ705663 BE831364 AJ713328 M21130 AW236257 BE831398 
    AW291977 BE831403 BP429396 BE831385 BM725836 AW468012 BC027917 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™, 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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    DEFA3 expression in normal human tissues (normalized intensities)
    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
     selected tissues (see all 2) fully expand
     
     Epidermis (Integumentary System)
             Full-thickness skin substitutes
     
     Blood (Hematopoietic System)
             Granulocytes Peripheral Blood
    DEFA3 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DEFA3 Protein Expression

    SOURCE GeneReport for Unigene cluster: Hs.654448
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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 human and chimp.

    Orthologs for DEFA3 gene from 1 species (see representative species )    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    chimpanzee
    (Pan troglodytes)
    Mammalia DEFA46
    Pan troglodytes defensin, alpha 4, corticostatin (...
    67(a)
    1 → many
    8(6919082-7015029)


    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)
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    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

    Find genes that share paralogs with DEFA3           About GenesLikeMe



    (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 DEFA3 (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) Selected 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

    Site Specific Mutation Identification with PCR Assays
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    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 604522    OMIM disorders: --

    4 diseases for DEFA3:    
    About MalaCards
    bell's palsy    multidrug-resistant tuberculosis    periodontal disease    idiopathic pulmonary fibrosis


    Find genes that share disorders with DEFA3           About GenesLikeMe

    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)
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    PubMed articles for DEFA3 gene, integrated from 10 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. (FEBS Lett. 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. (BMC Genomics 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. (Hum. Mol. Genet. 2005)
    4. Risk of meningioma and common variation in genes related to innate immunity. (PubMed id 20406964)1, 4 Rajaraman P....Inskip P.D. (amp 2010)
    5. Increased genomic copy number of DEFA1/DEFA3 is associated with susceptibility to severe sepsis in Chinese Han population. (PubMed id 20502117)1, 4 Chen Q....Fang X. (Anesthesiology 2010)
    6. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
    7. Copy number variation of defensin genes and HIV infection in Brazilian children. (PubMed id 19194307)1, 4 Milanese M....Crovella S. (J. Acquir. Immune Defic. Syndr. 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. (BMC Med. Genet. 2007)
    9. Antibacterial activity and specificity of the six human alpha- defensins. (PubMed id 15616305)1, 2 Ericksen B.... Lehrer R.I. (Antimicrob. Agents Chemother. 2005)
    10. 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. (Genome Res. 2004)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
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      Query String
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    OMIM
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      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 1668 HGNC: 2762 AceView: DEFA1andDEFA3 Ensembl:ENSG00000239839 euGenes: HUgn1668
    ECgene: DEFA3 Kegg: 1668 H-InvDB: DEFA3

    (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 DEFA3 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
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    Patent Information for DEFA3 gene:
    Search GeneIP for patents involving DEFA3

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



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