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DEFA1B Gene

protein-coding   GIFtS: 38
GCID: GC08M006854

Defensin, Alpha 1B

Microbiology & Infectious Diseases Congress
  See related disease
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 1B1 2     DEF13
HNP-12 3     DEFA23
HP-12 3     MRS3
HP12 3     Defensin, Alpha 13
Neutrophil Defensin 12     

External Ids:    HGNC: 335961   Entrez Gene: 7283582   Ensembl: ENSG000002402477   UniProtKB: P596653   

Export aliases for DEFA1B gene to outside databases

Previous GC identifer: GC08M006843


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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GeneCards Summary for DEFA1B Gene:
DEFA1B (defensin, alpha 1B) is a protein-coding gene. Diseases associated with DEFA1B include lung cancer. An important paralog of this gene is DEFA3.

UniProtKB/Swiss-Prot: DEF1_HUMAN, P59665
Function: Defensin 1 and defensin 2 have antibacterial, 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 DEFA1B 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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Regulatory elements:
   Search for regulatory transcription factor binding sites for DEFA1B
         Other transcription factors

Browse SwitchGear Promoter luciferase reporter plasmids
   Search Chromatin IP Primers for DEFA1B

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DEFA1B


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

DEFA1B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFA1B gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M006854:  view genomic region     (about GC identifiers)

Start:
6,854,288 bp from pter      End:
6,875,778 bp from pter
Size:
21,491 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: DEF1_HUMAN, P59665 (See protein sequence)
Recommended Name: Neutrophil defensin 1 precursor  
Size: 94 amino acids; 10201 Da
Subunit: Dimer
Selected PDB 3D structures from and Proteopedia for DEFA1B (see all 18):
2KHT (3D)        2PM1 (3D)        3GNY (3D)        3H6C (3D)        3HJ2 (3D)        3HJD (3D)    
Secondary accessions: P11479 Q14125 Q6EZF6

Explore the universe of human proteins at neXtProt for DEFA1B: NX_P59665

Explore proteomics data for DEFA1B at MOPED

Post-translational modifications: 

  • ADP-ribosylation drastically reduces cytotoxic and antibacterial activities, and enhances IL8 production1
  • Phosphorylation at Tyr-85 has been found in some cancer cell lines, and interferes with ADP-ribosylation1
  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus

  • See DEFA1B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins: NP_001035965.1  
    ENSEMBL proteins: 
     ENSP00000372136   ENSP00000443526  
    Reactome Protein details: P59665

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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 P59665

    ProtoNet protein and cluster: P59665

    1 Blocks protein domain: IPB002366 Defensin propeptide

    UniProtKB/Swiss-Prot: DEF1_HUMAN, P59665
    Similarity: Belongs to the alpha-defensin family


    DEFA1B 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: DEF1_HUMAN, P59665
    Function: Defensin 1 and defensin 2 have antibacterial, 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

    Animal Models:

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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
    DEF1_HUMAN, P59665: Secreted
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    extracellular5
    golgi apparatus4
    lysosome4
    vacuole4
    plasma membrane1

    Gene Ontology (GO): Selected cellular component terms (see all 6):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005576extracellular region TAS--
    GO:0005615extracellular space IDA--
    GO:0005796Golgi lumen TAS--
    GO:0031012colocalizes with extracellular matrix IDA--
    GO:0035578azurophil granule lumen TAS--

    DEFA1B 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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    SuperPaths for DEFA1B About    
    See pathways by source

    SuperPathContained pathways About
    1Defensins
    Defensins0.80
    Alpha-defensins0.00
    2Cellular roles of Anthrax toxin
    Cellular roles of Anthrax toxin

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways


    1 BioSystems Pathway for DEFA1B
        Cellular roles of Anthrax toxin

    2 Reactome Pathways for DEFA1B
        Defensins
    Alpha-defensins



    DEFA1B for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DEFA1B
    Interactions:

        Search GeneGlobe Interaction Network for DEFA1B

    STRING Interaction Network Preview (showing 4 interactants - click image to see more details)

    Selected Interacting proteins for DEFA1B (P596652, 3 ENSP000003721364) via UniProtKB, MINT, STRING, and/or I2D (see all 11)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    GSK3BP498412, 3MINT-8257086 I2D: score=2 
    PFDN1O609253I2D: score=3 
    C1QBP027463I2D: score=1 
    DEFA3P596663I2D: score=1 
    MMP14P502813I2D: score=1 
    About this table

    Gene Ontology (GO): Selected biological process terms (see all 10):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0006935chemotaxis TAS10914484
    GO:0006952defense response ----
    GO:0006955immune response TAS10914484
    GO:0019731antibacterial humoral response IDA15616305
    GO:0030520intracellular estrogen receptor signaling pathway IDA--

    DEFA1B 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 DEFA1B (DEF1)



    (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 DEFA1B gene: 
    NM_001042500.1  

    2 Ensembl transcripts including schematic representations, and UCSC links where relevant:
    ENST00000382689(uc003wqx.1) ENST00000535841
    Congresses - knowledge worth sharing:
    European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

    miRNA
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      QuantiTect SYBR Green Assays in human, mouse, rat DEFA1B
      QuantiFast Probe-based Assays in human, mouse, rat DEFA1B

    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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    DEFA1B expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: --
    DEFA1B Expression
    About this image

    DEFA1B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DEFA1B Protein Expression
        Custom PCR Arrays for DEFA1B
    Primer
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DEFA1B

    (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 DEFA1B 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 (...
    68(a)
    1 → many
    8(6919082-7015029)


    ENSEMBL Gene Tree for DEFA1B (if available)
    TreeFam Gene Tree for DEFA1B (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DEFA1B gene
    DEFA11 2  DEFA31 2  DEFA62  DEFA42  DEFA52  
    5 SIMAP similar genes for DEFA1B using alignment to 1 protein entry:     DEF1_HUMAN:
    DEFA3    DEFA4    DEFA5    DEFA6    Em

    DEFA1B 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 DEFA1B (see all 37)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 8 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs1507321571,2
    C--6856401(+) AGACCC/TGTGAT 1 -- int10--------
    rs1390436101,2
    C--6856441(+) TGTGTG/TTTTAG 1 -- int10--------
    rs3763276161,2
    C--6856786(+) CCGGGG/TTACTT 1 -- us2k10--------
    rs624874711,2
    C--6856995(+) CTGAAC/GTACCT 1 -- us2k10--------
    rs26157801,2
    C--6857020(-) GAGGCT/CTTAAA 1 -- us2k12Minor allele frequency- C:0.25NA 4
    rs29793941,2
    C,F--6857091(-) GTGTGC/TAGGTG 1 -- us2k13Minor allele frequency- T:0.50NA 6
    rs2013287931,2
    C--6857144(+) ACCTGA/GGGTCT 1 -- us2k10--------
    rs29793921,2
    C,F,H--6857162(-) TCATTG/ACTTTT 1 -- us2k113Minor allele frequency- A:0.06NS EA NA 1866
    rs285150271,2
    C--6857213(+) TGAGAC/ATGAGT 1 -- us2k14Minor allele frequency- A:0.00NA 8
    rs3704697241,2
    C--6857347(+) TTAAGC/GTAAAC 1 -- us2k10--------

    HapMap Linkage Disequilibrium report for DEFA1B (6854288 - 6875778 bp)

    Structural Variations
         Database of Genomic Variants (DGV) Selected variations for DEFA1B (see all 29):    About this table    
    Variant IDTypeSubtypePubMed ID
    nsv435861CNV Deletion17901297
    esv2736554CNV Deletion23290073
    nsv820476CNV Duplication20802225
    nsv471499CNV Duplication19718026
    nsv509248CNV Insertion20534489
    nsv6064CNV Insertion18451855
    nsv890070CNV Loss21882294
    nsv437041CNV Loss16327808
    nsv6060CNV Loss18451855
    nsv21CNV Loss15895083

    Site Specific Mutation Identification with PCR Assays
    Search QIAGEN SeqTarget long-range PCR primers for resequencing DEFA1B
    DNA2.0 Custom Variant and Variant Library Synthesis for DEFA1B

    (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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    1 disease for DEFA1B:    
    About MalaCards
    lung cancer


    DEFA1B for disorders           About GeneDecksing


    Export disorders for DEFA1B 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 DEFA1B gene, integrated from 10 sources (see all 24):
    (articles sorted by number of sources associating them with DEFA1B)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Toward understanding the cationicity of defensins. Arg and Lys versus their noncoded analogs. (PubMed id 17452329)1, 2 Zou G.... Lu W. (J. Biol. Chem. 2007)
    2. Antibacterial activity and specificity of the six human alpha- defensins. (PubMed id 15616305)1, 2 Ericksen B.... Lehrer R.I. (Antimicrob. Agents Chemother. 2005)
    3. Copy number polymorphism and expression level variation of the human alpha-defensin genes DEFA1 and DEFA3. (PubMed id 15944200)1, 3 Aldred P.M....Armour J.A. (Hum. Mol. Genet. 2005)
    4. 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)
    5. Signal peptide prediction based on analysis of experimentally verified cleavage sites. (PubMed id 15340161)1, 2 Zhang Z. and Henzel W.J. (Protein Sci. 2004)
    6. Inheritance of unequal numbers of the genes encoding the human neutrophil defensins HP-1 and HP-3. (PubMed id 8530462)1, 2 Mars W.M....Saunders G.F. (J. Biol. Chem. 1995)
    7. The structure of neutrophil defensin genes. (PubMed id 8325384)1, 2 Linzmeier R....Ganz T. (FEBS Lett. 1993)
    8. The structure of neutrophil defensin genes. (PubMed id 8477861)1, 2 Linzmeier R.... Ganz T. (FEBS Lett. 1993)
    9. NMR studies of defensin antimicrobial peptides. 1. Resonance assignment and secondary structure determination of rabbit NP-2 and human HNP-1. (PubMed id 1445872)1, 2 Zhang X.-L.... Pardi A. (Biochemistry 1992)
    10. NMR studies of defensin antimicrobial peptides. 2. Three-dimensional structures of rabbit NP-2 and human HNP-1. (PubMed id 1445873)1, 2 Pardi A.... Yip P.F. (Biochemistry 1992)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (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: 728358 HGNC: 33596 Ensembl:ENSG00000240247 euGenes: HUgn728358 ECgene: DEFA1B
    H-InvDB: DEFA1B

    (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 DEFA1B 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 DEFA1B gene:
    Search GeneIP for patents involving DEFA1B

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



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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    GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014

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