Human Gene DEFB110 (uc011dwr.2)
  Description: Homo sapiens defensin, beta 110 locus (DEFB110), transcript variant 2, mRNA.
RefSeq Summary (NM_001037728): Defensins form a family of antimicrobial 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. Two transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2014].
Transcript (Including UTRs)
   Position: hg19 chr6:49,976,851-49,989,694 Size: 12,844 Total Exon Count: 2 Strand: -
Coding Region
   Position: hg19 chr6:49,976,851-49,989,648 Size: 12,798 Coding Exon Count: 2 

Page IndexSequence and LinksPrimersGenetic AssociationsGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesmRNA DescriptionsPathways
Other NamesModel InformationMethods
Data last updated at UCSC: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr6:49,976,851-49,989,694)mRNA (may differ from genome)Protein (62 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCHPRDLynxMGIPubMedReactome
TreefamUniProtKBBioGrid CRISPR DB

-  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


-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DEFB110
CDC HuGE Published Literature: DEFB110
Positive Disease Associations: Tunica Media
Related Studies:
  1. Tunica Media
    , , . [PubMed 0]

+  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: 0.00 RPKM in Adipose - Subcutaneous
Total median expression: 0.00 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -10.0046-0.217 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
  ModBase Predicted Comparative 3D Structure on Q30KQ9-2
FrontTopSide
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 DetailsGene Details    
Gene SorterGene Sorter    
 RGD    
 Protein Sequence    
 Alignment    

-  Descriptions from all associated GenBank mRNAs
  DQ012014 - Homo sapiens beta-defensin 110 (DEFB110) mRNA, complete cds.
BC148763 - Synthetic construct Homo sapiens clone IMAGE:100015799, MGC:183176 defensin, beta 110 (DEFB110) mRNA, encodes complete protein.
BC141478 - Synthetic construct Homo sapiens clone IMAGE:100014708, MGC:175343 defensin, beta 110 (DEFB110) mRNA, encodes complete protein.
DQ012015 - Homo sapiens beta-defensin 111 (DEFB111) mRNA, complete cds.
BC156744 - Synthetic construct Homo sapiens clone IMAGE:100062285, MGC:190230 defensin, beta 111 (DEFB111) mRNA, encodes complete protein.
BC148541 - Synthetic construct Homo sapiens clone IMAGE:100015486, MGC:183056 defensin, beta 111 (DEFB111) mRNA, encodes complete protein.

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

Protein Q30KQ9 (Reactome details) participates in the following event(s):

R-HSA-1471322 Beta-defensins are secreted
R-HSA-1461973 Defensins
R-HSA-1461957 Beta 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: DEFB10, DEFB11, DEFB111, NM_001037728, NP_001032817, Q30KQ9-2
UCSC ID: uc011dwr.2
RefSeq Accession: NM_001037728
Protein: Q30KQ9-2, splice isoform of Q30KQ9 CCDS: CCDS43473.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_001037728.2
exon count: 2CDS single in 3' UTR: no RNA size: 235
ORF size: 189CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 577.00frame 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.