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DEFB104B Gene

protein-coding   GIFtS: 38
GCID: GC08M007317

Defensin, Beta 104B

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, Beta 104B1 2     hBD-42 3
Beta-Defensin 42 3     Beta-Defensin 1042
Defensin, Beta 1042 3     DEFB1043
BD-42 3     DEFB43
DEFB-42 3     

External Ids:    HGNC: 261651   Entrez Gene: 5036182   Ensembl: ENSG000001770237   UniProtKB: Q8WTQ13   

Export aliases for DEFB104B gene to outside databases

Previous GC identifer: GC08U900557


(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 DEFB104B Gene:
Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Defensins are short, processed
peptide molecules that are classified by structure into three groups: alpha-defensins, beta-defensins and
theta-defensins. All beta-defensin genes are densely clustered in four to five syntenic chromosomal regions.
Chromosome 8p23 contains at least two copies of the duplicated beta-defensin cluster. This duplication results in
two identical copies of defensin, beta 104, DEFB104A and DEFB104B, in head-to-head orientation. This gene,
DEFB104B, represents the more telomeric copy. (provided by RefSeq, Jul 2008)

GeneCards Summary for DEFB104B Gene:
DEFB104B (defensin, beta 104B) is a protein-coding gene. Diseases associated with DEFB104B include thyroiditis. An important paralog of this gene is DEFB104A.

UniProtKB/Swiss-Prot: D104A_HUMAN, Q8WTQ1
Function: Has antimicrobial activity. Synergistic effects with lysozyme and DEFB103




(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:
   Regulatory transcription factor binding sites in the DEFB104B gene promoter:
         C/EBPbeta   Pbx1a   CUTL1   AREB6   S8   POU2F1   POU2F1a   Chx10   Cart-1   Pax-4a   
         Other transcription factors

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Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DEFB104B


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

DEFB104B Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DEFB104B gene location

GeneLoc information about chromosome 8         GeneLoc Exon Structure

GeneLoc location for GC08M007317:  view genomic region     (about GC identifiers)

Start:
7,327,830 bp from pter      End:
7,332,604 bp from pter
Size:
4,775 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: D104A_HUMAN, Q8WTQ1 (See protein sequence)
Recommended Name: Beta-defensin 104 precursor  
Size: 72 amino acids; 8526 Da
Secondary accessions: Q496I2 Q496I3 Q496I4

Explore the universe of human proteins at neXtProt for DEFB104B: NX_Q8WTQ1

Explore proteomics data for DEFB104B at MOPED


See DEFB104B Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

REFSEQ proteins: NP_001035792.1  
ENSEMBL proteins: 
 ENSP00000322191  
Reactome Protein details: Q8WTQ1

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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:
DEFB: Defensins, beta

1 InterPro protein domain:
 IPR025933 Beta_defensin

Graphical View of Domain Structure for InterPro Entry Q8WTQ1

ProtoNet protein and cluster: Q8WTQ1

UniProtKB/Swiss-Prot: D104A_HUMAN, Q8WTQ1
Similarity: Belongs to the beta-defensin family


DEFB104B 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: D104A_HUMAN, Q8WTQ1
Function: Has antimicrobial activity. Synergistic effects with lysozyme and DEFB103
Induction: Antimicrobial activity is decreased when the sodium chloride concentration is increased

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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
D104A_HUMAN, Q8WTQ1: Secreted
Subcellular locations from COMPARTMENTS: 

CompartmentConfidence
extracellular5
nucleus1

Gene Ontology (GO): 1 cellular component term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0005576extracellular region IEA--

DEFB104B 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 DEFB104B About                                                                                                See pathways by source

SuperPathContained pathways About
1Defensins
Defensins0.80
Beta defensins0.80

Pathways by source                                                                                                                                                                 See SuperPaths
Show all pathways



2 Reactome Pathways for DEFB104B
    Defensins
Beta defensins



DEFB104B for pathways           About GeneDecksing

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Interactions:

    Search GeneGlobe Interaction Network for DEFB104B

Gene Ontology (GO): 1 biological process term:    About this table

GO IDQualified GO termEvidencePubMed IDs
GO:0042742defense response to bacterium IEA--

DEFB104B 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 Tocris compounds for DEFB104B (D104A)



(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 DEFB104B gene: 
NM_001040702.1  

1 Ensembl transcript including schematic representation, and UCSC links where relevant:
ENST00000316169(uc003wrn.3)
Congresses - knowledge worth sharing:
European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) 10 - 13 May 2014

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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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DEFB104B expression in normal human tissues (normalized intensities)
See probesets specificity/sensitivity at GeneAnnot
About this imageBioGPS <intensity>2/3
CGAP TAG: CTGTTTGAGA
DEFB104B Expression
About this image

DEFB104B Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

DEFB104B Protein Expression

UniProtKB/Swiss-Prot: D104A_HUMAN, Q8WTQ1
Tissue specificity: High expression in the testis. Gastric antrum exhibited relatively high levels. A lower
expression is observed in uterus and neutrophils thyroid gland, lung, and kidney. No detectable expression in
other tissues tested

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In Situ
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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 DEFB104B gene from 1 species (see representative species )    About this table
Organism Taxonomic
classification
Gene Description Human
Similarity
Orthology
Type
Details
chimpanzee
(Pan troglodytes)
Mammalia DEFB1041 defensin, beta 104 100(n)
100(a)
  735929  NM_001113568.1  NP_001107040.1 


ENSEMBL Gene Tree for DEFB104B (if available)
TreeFam Gene Tree for DEFB104B (if available)

(Paralogs according to 1HomoloGene,
2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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Paralogs for DEFB104B gene
DEFB104A1 2  
4 SIMAP similar genes for DEFB104B using alignment to 1 protein entry:     D104A_HUMAN:
DEFB108B    DEFB108P1    DEFB108P2    DEFB115

DEFB104B 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 DEFB104B (see all 102)    About this table    
Genomic DataTranscription Related DataAllele Frequencies
SNP IDValidClinical
significance
Chr 8 posSequence#AA
Chg
TypeMore#Allele
freq
PopTotal
sample
More
----------
rs2019037111,2
--7327932(+) CATGCA/GTAGGT 2 Y syn10--------
rs2005963771,2
--7327984(+) TCTTCC/TGGCAA 2 Q R mis10--------
rs2001186171,2
--7328067(+) TCATTA/CATTGC 1 -- int10--------
rs1901408051,2
--7328123(+) GGGGGA/GTAGAG 1 -- int10--------
rs1997253821,2
C--7328278(+) TCCCTA/GCAAGT 1 -- int10--------
rs2009215331,2
C--7328373(+) CAGACC/TCATGC 1 -- int10--------
rs2014470131,2
C--7328703(+) ATATAC/TACATA 1 -- int10--------
rs1995337521,2
C--7329018(+) ATGGAC/TTTAGC 1 -- int10--------
rs27400201,2
C--7329508(-) AAACTG/TCCTTT 1 -- int10--------
rs626397651,2
C,F--7329573(+) CACAGT/CGGGTG 1 -- int14Minor allele frequency- C:0.38WA NA CSA 8

HapMap Linkage Disequilibrium report for DEFB104B (7327830 - 7332604 bp)

Structural Variations
     Database of Genomic Variants (DGV) Selected variations for DEFB104B (see all 71):    About this table    
Variant IDTypeSubtypePubMed ID
esv2736558CNV Deletion23290073
dgv26n31CNV Duplication19718026
dgv25n31CNV Duplication19718026
nsv890270CNV Loss21882294
nsv890300CNV Loss21882294
dgv7694n71CNV Loss21882294
dgv7664n71CNV Loss21882294
nsv508496CNV Loss20534489
dgv7680n71CNV Loss21882294
dgv1170n67CNV Loss20364138

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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.)
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1 disease for DEFB104B:    About MalaCards
thyroiditis


DEFB104B for disorders           About GeneDecksing


Export disorders for DEFB104B 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 DEFB104B gene, integrated from 10 sources (see all 11):
(articles sorted by number of sources associating them with DEFB104B)
    Utopia: connect your pdf to the dynamic
world of online information

  1. Human beta-defensin 4: a novel inducible peptide with a specific salt-sensitive spectrum of antimicrobial activity. (PubMed id 11481241)1, 2 Conejo-Garcia J.-R....Forssmann W.-G. (FASEB J. 2001)
  2. Expression of I^-defensin-4 in &quot;an in vivo and ex vivo model&quot; of human osteoarthritic knee meniscus. (PubMed id 21879330)1 Musumeci G....Loreto C. (Knee Surg Sports Traumatol Arthrosc 2012)
  3. Copy number variation of I^-defensin genes in BehAset's disease. (PubMed id 21385545)1 Park J.J....Lee E.B. (Clin. Exp. Rheumatol. 2011)
  4. Cross-species analysis of the mammalian beta-defensin gene family: presence of syntenic gene clusters and preferential expression in the male reproductive tract. (PubMed id 16033865)1 Patil A.A.... Zhang G. (Physiol. Genomics 2005)
  5. Polymorphic segmental duplications at 8p23.1 challenge the determination of individual defensin gene repertoires and the assembly of a contiguous human reference sequence. (PubMed id 15588320)1 Taudien S....Platzer M. (BMC Genomics 2004)
  6. Evidence for duplication of the human defensin gene DEFB4 in chromosomal region 8p22-23 and implications for the analysis of SNP allele distribution. (PubMed id 15727258)1 Boniotto M....Gallagher G. (Genet. Test. 2004)
  7. 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)
  8. Extensive normal copy number variation of a beta-defensin antimicrobial-gene cluster. (PubMed id 12916016)1 Hollox E.J....Barber J.C. (Am. J. Hum. Genet. 2003)
  9. Duplication and selection in the evolution of primate beta-defensin genes. (PubMed id 12734011)1 Semple C.A.M.... Dorin J.R. (Genome Biol. 2003)
  10. Identification of multiple novel epididymis-specific beta-defensin isoforms in humans and mice. (PubMed id 12193721)1 Yamaguchi Y.... Ouchi Y. (J. Immunol. 2002)

(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: 503618 HGNC: 26165 Ensembl:ENSG00000177023 euGenes: HUgn503618 ECgene: DEFB104B
H-InvDB: DEFB104B

(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 DEFB104B 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 DEFB104B gene:
Search GeneIP for patents involving DEFB104B

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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