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DEFA6 Gene

protein-coding   GIFtS: 52
GCID: GC08M006769

Defensin, Alpha 6, Paneth Cell-Specific

  See DEFA6-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 6, Paneth Cell-Specific1 2
DEF62 3 5
HD-62
Defensin 62
defensin-62
Defensin, Alpha 63

External Ids:    HGNC: 27651   Entrez Gene: 16712   Ensembl: ENSG000001648227   OMIM: 6004715   UniProtKB: Q015243   

Export aliases for DEFA6 gene to outside databases

Previous GC identifers: GC08M006846 GC08M007036 GC08M006942 GC08M006562


(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 DEFA6 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. Several alpha defensin genes appear to be
clustered on chromosome 8. The protein encoded by this gene, defensin, alpha 6, is highly expressed in the
secretory granules of Paneth cells of the small intestine, and likely plays a role in host defense of human
bowel. (provided by RefSeq, Jul 2008)

GeneCards Summary for DEFA6 Gene:
DEFA6 (defensin, alpha 6, Paneth cell-specific) is a protein-coding gene. Diseases associated with DEFA6 include childhood leukemia. An important paralog of this gene is DEFA1B.

UniProtKB/Swiss-Prot: DEF6_HUMAN, Q01524
Function: Has very low antimicrobial activity against Gram-negative and Gram-positive bacteria. May protect cells
against infection with HIV-1

Gene Wiki entry for DEFA6 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 DEFA6 gene promoter:
         TBP   AREB6   Nkx2-5   POU3F2 (N-Oct-5b)   POU3F2 (N-Oct-5a)   POU3F2   C/EBPalpha   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDEFA6 promoter sequence
   Search Chromatin IP Primers for DEFA6

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DEFA6


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

DEFA6 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFA6 gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M006769:  view genomic region     (about GC identifiers)

Start:
6,782,215 bp from pter      End:
6,783,598 bp from pter
Size:
1,384 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: DEF6_HUMAN, Q01524 (See protein sequence)
Recommended Name: Defensin-6 precursor  
Size: 100 amino acids; 10975 Da
Subunit: Homodimer
2 PDB 3D structures from and Proteopedia for DEFA6:
1ZMQ (3D)        3QTE (3D)    
Secondary accessions: Q6EZF9

Explore the universe of human proteins at neXtProt for DEFA6: NX_Q01524

Explore proteomics data for DEFA6 at MOPED


See DEFA6 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001917.1  
ENSEMBL proteins: 
 ENSP00000297436  
Reactome Protein details: Q01524

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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 Q01524

ProtoNet protein and cluster: Q01524

1 Blocks protein domain: IPB002366 Defensin propeptide

UniProtKB/Swiss-Prot: DEF6_HUMAN, Q01524
Similarity: Belongs to the alpha-defensin family


Find genes that share domains with DEFA6           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: DEF6_HUMAN, Q01524
Function: Has very low antimicrobial activity against Gram-negative and Gram-positive bacteria. May protect cells
against infection with HIV-1

     Genatlas biochemistry entry for DEFA6:
defensin alpha 6,3-4kDa,enteric Paneth cells,released from azurophil granules of Paneth cells,oxygen independent
phagocytosis of Gram+,Gram- bacteria,many fungi,some viruses

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
DEF6_HUMAN, Q01524: Secreted
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
golgi apparatus4
nucleus1

Gene Ontology (GO): 3 cellular component terms:    About this table

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

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(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 DEFA6 About    
See pathways by source

SuperPathContained pathways About
1Defensins
Defensins0.80
Alpha-defensins0.00


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Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



2 Reactome Pathways for DEFA6
    Defensins
Alpha-defensins


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Interactions:

    Search GeneGlobe Interaction Network for DEFA6

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

4 Interacting proteins for DEFA6 (ENSP000002974364) via UniProtKB, MINT, STRING, and/or I2D
InteractantInteraction Details
GeneCardExternal ID(s)
DEFA4ENSP000002974354STRING: ENSP00000297435
DEFA5ENSP000003298904STRING: ENSP00000329890
DEFB1ENSP000002974394STRING: ENSP00000297439
DEFB4AENSP000003035324STRING: ENSP00000303532
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Gene Ontology (GO): Selected biological process terms (see all 6):    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0006952defense response ----
GO:0019731antibacterial humoral response IDA15616305
GO:0031640killing of cells of other organism IEA--
GO:0042742defense response to bacterium ----
GO:0045087innate immune response TAS--

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(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 DEFA6 (DEF6)

1 Novoseek inferred chemical compound relationship for DEFA6 gene    About this table
Compound   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
hbd2 91.8 4 14568394 (2), 19549264 (1), 10964161 (1)



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(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,
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REFSEQ mRNAs for DEFA6 gene: 
NM_001926.3  

Unigene Cluster for DEFA6:

Defensin, alpha 6, Paneth cell-specific
Hs.711  [show with all ESTs]
Unigene Representative Sequence: NM_001926
1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000297436(uc003wqt.3)
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Additional mRNA sequence: 

BC069667.1 BC069710.1 BC069728.1 BC069769.1 BC093951.1 BC093953.1 M98331.1 

2 DOTS entries:

DT.102820200  DT.106012 

10 AceView cDNA sequences:

T29657 M98331 BC069710 BM986901 BC069769 BC069728 NM_001926 BC069667 
BM855691 AW951409 

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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DEFA6 expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: GGTATTAACC
DEFA6 Expression
About this image

DEFA6 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

DEFA6 Protein Expression

SOURCE GeneReport for Unigene cluster: Hs.711

UniProtKB/Swiss-Prot: DEF6_HUMAN, Q01524
Tissue specificity: Paneth cells of the small intestine

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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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  --

ENSEMBL Gene Tree for DEFA6 (if available)
TreeFam Gene Tree for DEFA6 (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DEFA6 gene
DEFA1B2  DEFA32  DEFA42  DEFA12  DEFA52  
6 SIMAP similar genes for DEFA6 using alignment to 1 protein entry:     DEF6_HUMAN:
DEFA4    DEFA5    DEFA1    DEFA1B    DEFA3    Em

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1 Pseudogenes.org Pseudogene for DEFA6
PGOHUM00000249207


(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 DEFA6 (see all 158)    About this table                                 

Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs1930669991,2
--6781757(+) ACGTGC/TGGTGG 1 -- ds50010--------
rs1846335021,2
--6781758(+) CGTGCA/GGTGGC 1 -- ds50010--------
rs1891492331,2
--6781827(+) GAGTTC/TGAGAC 1 -- ds50010--------
rs1813778131,2
--6781899(+) TGGTGC/GATACC 1 -- ds50010--------
rs1855433471,2
--6781937(+) GGCAGA/GAGAAT 1 -- ds50010--------
rs38881521,2
C,F,A,H--6781962(+) AGGTAA/GAGGTT 1 -- ds50016Minor allele frequency- G:0.28NA WA 18
rs1460000571,2
--6782201(+) GAAAAC/GCACAA 1 -- ds50010--------
rs1162365991,2
C,F--6782204(+) AAGCAC/GAAACA 1 -- ds50010--------
rs7122761,2
C,F,O,A,H--6782271(-) TGTCCT/CATACA 1 -- ut31 ese338Minor allele frequency- C:0.10MN NS EA NA CSA WA 4124
rs562399091,2
C,F--6782279(-) CTGTCG/ATGTGT 1 -- ut313Minor allele frequency- A:0.05CSA WA 122

HapMap Linkage Disequilibrium report for DEFA6 (6782215 - 6783598 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for DEFA6 (see all 14):    About this table    
Variant IDTypeSubtypePubMed ID
nsv509248CNV Insertion20534489
nsv890064CNV Gain21882294
nsv465436CNV Gain19166990
nsv831221CNV Gain17160897
nsv528374CNV Gain19592680
esv2752262CNV Gain17911159
nsv890066CNV Gain21882294
nsv465437CNV Gain19166990
dgv7656n71CNV Gain21882294
dgv7657n71CNV Gain21882294

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(in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Novoseek, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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OMIM gene information: 600471    OMIM disorders: --

1 disease for DEFA6:    
About MalaCards
childhood leukemia

1 disease from the University of Copenhagen DISEASES database for DEFA6:
Crohn's disease

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1 Novoseek inferred disease relationship for DEFA6 gene    About this table

Disease   -log (P-Val)   Hits   PubMed IDs for Articles with Shared Sentences (# sentences)
inflammation 21.5 4 15479689 (1), 12519391 (1), 19549264 (1), 18810765 (1)

Genetic Association Database (GAD): DEFA6
Human Genome Epidemiology (HuGE) Navigator: DEFA6 (8 documents)

Export disorders for DEFA6 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 DEFA6 gene, integrated from 10 sources (see all 55):
(articles sorted by number of sources associating them with DEFA6)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Defensin-6 mRNA in human Paneth cells: implications for antimicrobial peptides in host defense of the human bowel. (PubMed id 8417977)1, 2, 3, 9 Jones D.E. and Bevins C.L. (FEBS Lett. 1993)
  2. Human enteric defensins. Gene structure and developmental expression. (PubMed id 8626737)1, 2, 9 Mallow E.B.... Bevins C.L. (J. Biol. Chem. 1996)
  3. Crystal structures of human alpha-defensins HNP4, HD5, and HD6. (PubMed id 17088326)1, 2, 9 Szyk A.... Lubkowski J. (Protein Sci. 2006)
  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. Polymorphisms in innate immunity genes and risk of childhood leukemia. (PubMed id 20438785)1, 4 Han S....Kang D. (Hum. Immunol. 2010)
  6. 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)
  7. Single nucleotide polymorphisms and the haplotype in the DEFB1 gene are associated with atopic dermatitis in a Korean population. (PubMed id 19135873)1, 4 Kim E....Yang J.M. (J. Dermatol. Sci. 2009)
  8. Antibacterial activity and specificity of the six human alpha- defensins. (PubMed id 15616305)1, 2 Ericksen B.... Lehrer R.I. (Antimicrob. Agents Chemother. 2005)
  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. (Genome Res. 2004)
  10. Innate immunity and non-Hodgkin's lymphoma (NHL) related genes in a nested case-control study for gastric cancer risk. (PubMed id 23028900)1 Park S.K....Kang D. (PLoS ONE 2012)

(in PubMed, OMIM, and NCBI Bookshelf)
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 ANDOR
Aliases
Disorders
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: 1671 HGNC: 2765 AceView: DEFA6 Ensembl:ENSG00000164822 euGenes: HUgn1671
ECgene: DEFA6 H-InvDB: DEFA6

(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 DEFA6 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 DEFA6 gene:
Search GeneIP for patents involving DEFA6

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, eBioscience, antibodies-online, and/or others, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Addgene, Cell lines from GenScript, and ESI BIO, Flow cytometery from eBioscience, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
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 Custom PCR Arrays for DEFA6 Search Chromatin IP Primers for DEFA6
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 Vector-based siRNA and miRNA, Ready for Transfection Gene Mutant Library, Variants up to 10^11
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 Search Tocris compounds for DEFA6 (DEF6)
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 Search www.enzolifesciences.com for proteins, assays, substrates, inhibitors & antibodies

 Novus Tissue Slides
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 Browse ESI BIO Cell Lines and PureStem Progenitors for DEFA6
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 antibodies-online antibodies for DEFA6 (21 products)
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 antibodies-online proteins for DEFA6 (2 products)
       
GeneCards Homepage - Last full update: 7 May 2014 - Incrementals: 9 May 2014 , 2 Jun 2014 , 26 Jun 2014 , 30 Jun 2014 , 21 Aug 2014 , 8 Sep 2014 , 7 Oct 2014

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