Human Gene DEFA4 (uc003wqu.1) Description and Page Index
  Description: Homo sapiens defensin, alpha 4, corticostatin (DEFA4), mRNA.
RefSeq Summary (NM_001925): Defensins are a family of antimicrobial 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 are clustered on chromosome 8. This gene differs from other genes of this family by an extra 83-base segment that is apparently the result of a recent duplication within the coding region. The protein encoded by this gene, defensin, alpha 4, is found in the neutrophils; it exhibits corticostatic activity and inhibits corticotropin stimulated corticosterone production. [provided by RefSeq, Oct 2014]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: HY078510.1, DN998607.1 [ECO:0000332] RNAseq introns :: single sample supports all introns SAMEA1965299, SAMEA2142853 [ECO:0000348] ##Evidence-Data-END## ##RefSeq-Attributes-START## Protein has antimicrobial activity :: PMID: 2500436 RefSeq Select criteria :: based on single protein-coding transcript ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr8:6,793,345-6,795,786 Size: 2,442 Total Exon Count: 3 Strand: -
Coding Region
   Position: hg19 chr8:6,793,542-6,794,421 Size: 880 Coding Exon Count: 2 

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

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr8:6,793,345-6,795,786)mRNA (may differ from genome)Protein (97 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblEntrez GeneExonPrimerGeneCardsGeneNetwork
HGNCHPRDLynxMGIneXtProtOMIM
PubMedReactomeStanford SOURCETreefamUniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DEF4_HUMAN
DESCRIPTION: RecName: Full=Neutrophil defensin 4; AltName: Full=Defensin, alpha 4; AltName: Full=HNP-4; Short=HP-4; Flags: Precursor;
FUNCTION: Has antimicrobial activity against Gram-negative bacteria, and to a lesser extent also against Gram-positive bacteria and fungi. Protects blood cells against infection with HIV-1 (in vitro). Inhibits corticotropin (ACTH)-stimulated corticosterone production.
SUBUNIT: Homodimer.
SUBCELLULAR LOCATION: Secreted.
SIMILARITY: Belongs to the alpha-defensin family.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DEFA4
CDC HuGE Published Literature: DEFA4

-  MalaCards Disease Associations
  MalaCards Gene Search: DEFA4
Diseases sorted by gene-association score: intestinal perforation (6)

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

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 31.05 RPKM in Whole Blood
Total median expression: 43.20 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 -8.8051-0.173 Picture PostScript Text
3' UTR -48.91197-0.248 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
IPR016327 - Alpha-defensin
IPR006080 - Defensin_beta/neutrophil
IPR002366 - Defensin_propep
IPR006081 - Mammalian_defensins

Pfam Domains:
PF00323 - Mammalian defensin
PF00879 - Defensin propeptide

Protein Data Bank (PDB) 3-D Structure
MuPIT help

1ZMM
- X-ray MuPIT


ModBase Predicted Comparative 3D Structure on P12838
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-  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 orthologNo orthologNo orthologNo orthologNo orthologNo ortholog
      
      
      
      
      

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0042803 protein homodimerization activity

Biological Process:
GO:0006952 defense response
GO:0010818 T cell chemotaxis
GO:0019730 antimicrobial humoral response
GO:0019731 antibacterial humoral response
GO:0019732 antifungal humoral response
GO:0031640 killing of cells of other organism
GO:0042742 defense response to bacterium
GO:0043312 neutrophil degranulation
GO:0045087 innate immune response
GO:0050829 defense response to Gram-negative bacterium
GO:0050830 defense response to Gram-positive bacterium
GO:0050832 defense response to fungus

Cellular Component:
GO:0005576 extracellular region
GO:0005615 extracellular space
GO:0005796 Golgi lumen
GO:0035580 specific granule lumen
GO:0042582 azurophil granule


-  Descriptions from all associated GenBank mRNAs
  X65977 - H.sapiens mRNA for corticostatin HP-4 precursor.
BC106747 - Homo sapiens defensin, alpha 4, corticostatin, mRNA (cDNA clone MGC:120099 IMAGE:40021796), complete cds.
JD358939 - Sequence 339963 from Patent EP1572962.
JD241368 - Sequence 222392 from Patent EP1572962.
BC093959 - Homo sapiens defensin, alpha 4, corticostatin, mRNA (cDNA clone MGC:120994 IMAGE:7939804), complete cds.
BC112091 - Homo sapiens defensin, alpha 4, corticostatin, mRNA (cDNA clone MGC:138296 IMAGE:8327559), complete cds.
KJ901380 - Synthetic construct Homo sapiens clone ccsbBroadEn_10774 DEFA4 gene, encodes complete protein.
JD392164 - Sequence 373188 from Patent EP1572962.
JD192506 - Sequence 173530 from Patent EP1572962.

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

Protein P12838 (Reactome details) participates in the following event(s):

R-HSA-1462003 HNP1-4 are stored in primary neutrophil granules
R-HSA-1462039 Pro-HNP1-4 are cleaved to biologically active defensin
R-HSA-1462014 Alpha-defensins form biologically active dimers
R-HSA-6798749 Exocytosis of specific granule lumen proteins
R-HSA-1462041 HNP1-4 are released into phagocytic vacuoles
R-HSA-1461971 Alpha-defensin dimers adsorb onto microbial membrane anionic phospholipids
R-HSA-1462054 Alpha-defensins
R-HSA-6798695 Neutrophil degranulation
R-HSA-1461973 Defensins
R-HSA-168249 Innate Immune System
R-HSA-6803157 Antimicrobial peptides
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: DEF4, DEF4_HUMAN, NM_001925, NP_001916, P12838
UCSC ID: uc003wqu.1
RefSeq Accession: NM_001925
Protein: P12838 (aka DEF4_HUMAN)
CCDS: CCDS5961.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001925.1
exon count: 3CDS single in 3' UTR: no RNA size: 542
ORF size: 294CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 707.00frame 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
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-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.