Human Gene DEFB4A (uc003wsd.3)
  Description: Homo sapiens defensin, beta 4A (DEFB4A), mRNA.
RefSeq Summary (NM_004942): Defensins form a family of microbicidal and cytotoxic peptides made by neutrophils. Members of the defensin family are highly similar in protein sequence. This gene encodes defensin, beta 4, an antibiotic peptide which is locally regulated by inflammation. [provided by RefSeq, Jul 2008]. Sequence Note: The RefSeq transcript and protein were derived from genomic sequence to make the sequence consistent with the reference genome assembly. The genomic coordinates used for the transcript record were based on alignments.
Transcript (Including UTRs)
   Position: hg19 chr8:7,752,199-7,754,237 Size: 2,039 Total Exon Count: 2 Strand: +
Coding Region
   Position: hg19 chr8:7,752,235-7,754,132 Size: 1,898 Coding Exon Count: 2 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:7,752,199-7,754,237)mRNA (may differ from genome)Protein (64 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaAlphaFold
BioGPSEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMalacardsMGIneXtProt
OMIMPubMedReactomeTreefamUniProtKBWikipedia
BioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: DFB4A_HUMAN
DESCRIPTION: RecName: Full=Beta-defensin 4A; AltName: Full=Beta-defensin 2; Short=BD-2; Short=hBD-2; AltName: Full=Defensin, beta 2; AltName: Full=Skin-antimicrobial peptide 1; Short=SAP1; Flags: Precursor;
FUNCTION: Has antibacterial activity (Potential).
SUBCELLULAR LOCATION: Secreted.
TISSUE SPECIFICITY: Expressed in the skin and respiratory tract.
INDUCTION: By inflammation.
SIMILARITY: Belongs to the beta-defensin family. LAP/TAP subfamily.

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DEFB4A
Diseases sorted by gene-association score: oral candidiasis (30), tinea corporis (23), cervicitis (21), urethritis (20), dermatophytosis (16), vulvovaginal candidiasis (13), cholesteatoma of middle ear (12), candidiasis (11), corneal abscess (11), cholesteatoma (10), microsporidiosis (10), lichen planus (9), septic arthritis (9), tinea cruris (9), anal fistula (9), acne (9), eumycotic mycetoma (8), salmonellosis (8), folliculitis (8), bacterial vaginosis (8), aleutian mink disease (7), leukoplakia (7), cellulitis (7), sinusitis (6), sebaceous gland disease (6), osteonecrosis of the jaw (6), gingivitis (6), esophageal candidiasis (6), dermatomycosis (6), bronchiolitis obliterans (6), vaginal disease (5), atopic dermatitis (4), gastritis (4), periodontal disease (3), cystic fibrosis (3), eye disease (1)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 1.33 RPKM in Esophagus - Mucosa
Total median expression: 1.53 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -6.6036-0.183 Picture PostScript Text
3' UTR -26.30105-0.250 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001855 - Defensin_beta-typ
IPR006080 - Defensin_beta/neutrophil

Pfam Domains:
PF00711 - Beta defensin

SCOP Domains:
57392 - Defensin-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help
1E4Q - NMR 1FD3 - X-ray 1FD4 - X-ray 1FQQ - NMR MuPIT


ModBase Predicted Comparative 3D Structure on O15263
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The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserNo orthologNo orthologNo orthologNo ortholog
 Gene Details    
 Gene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0005515 protein binding
GO:0031731 CCR6 chemokine receptor binding

Biological Process:
GO:0006935 chemotaxis
GO:0006952 defense response
GO:0006955 immune response
GO:0007186 G-protein coupled receptor signaling pathway
GO:0019730 antimicrobial humoral response
GO:0031640 killing of cells of other organism
GO:0042742 defense response to bacterium
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005622 intracellular
GO:0005796 Golgi lumen


-  Descriptions from all associated GenBank mRNAs
  LP896502 - Sequence 1366 from Patent EP3253886.
JD330057 - Sequence 311081 from Patent EP1572962.
BC069285 - Homo sapiens defensin, beta 4, mRNA (cDNA clone MGC:97415 IMAGE:7262691), complete cds.
BC093985 - Homo sapiens defensin, beta 4, mRNA (cDNA clone MGC:121020 IMAGE:7939830), complete cds.
BC093983 - Homo sapiens defensin, beta 4, mRNA (cDNA clone MGC:121018 IMAGE:7939828), complete cds.
Z71389 - H.sapiens mRNA for skin-antimicrobial-peptide 1 (SAP1).
KJ891044 - Synthetic construct Homo sapiens clone ccsbBroadEn_00438 DEFB4A gene, encodes complete protein.
JD310098 - Sequence 291122 from Patent EP1572962.
JD335027 - Sequence 316051 from Patent EP1572962.
JD437163 - Sequence 418187 from Patent EP1572962.
JD427452 - Sequence 408476 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O15263 (Reactome details) participates in the following event(s):

R-HSA-1973968 Beta-defensins 4A and 103 bind CCR2
R-HSA-1471338 Beta-defensins 1, 4A and 103 bind CCR6
R-HSA-1471322 Beta-defensins are secreted
R-HSA-1461957 Beta defensins
R-HSA-1461973 Defensins
R-HSA-6803157 Antimicrobial peptides
R-HSA-168249 Innate Immune System
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: DEFB102, DEFB2, DEFB4, DEFB4B, DFB4A_HUMAN, NM_004942, NP_001192195, O15263, Q52LC0
UCSC ID: uc003wsd.3
RefSeq Accession: NM_004942
Protein: O15263 (aka DFB4A_HUMAN)
CCDS: CCDS5971.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_004942.2
exon count: 2CDS single in 3' UTR: no RNA size: 336
ORF size: 195CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 590.00frame shift in genome: no % Coverage: 100.00
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.