Defb4 (defensin beta 4) - Rat Genome Database

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Gene: Defb4 (defensin beta 4) Rattus norvegicus
Analyze
Symbol: Defb4
Name: defensin beta 4
RGD ID: 619944
Description: Predicted to enable CCR6 chemokine receptor binding activity and chemoattractant activity. Predicted to be involved in cell chemotaxis; defense response to Gram-negative bacterium; and defense response to Gram-positive bacterium. Predicted to be active in extracellular space. Orthologous to several human genes including DEFB4A (defensin beta 4A); INTERACTS WITH bisphenol A (ortholog); cadmium atom (ortholog); cadmium dichloride (ortholog).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BD-2; BD-4; beta defensin-2; beta-defensin 3; beta-defensin 4; Defb2; Defb3; defensin beta 3; defensin, beta 4; RBD-2; RBD-4
RGD Orthologs
Human
Mouse
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,352,911 - 77,356,104 (-)NCBIGRCr8
mRatBN7.21670,650,472 - 70,653,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,650,472 - 70,653,665 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,927,305 - 75,930,496 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,390,193 - 79,393,646 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,639,631 - 74,643,084 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,634,598 - 75,637,789 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,634,598 - 75,637,789 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,234,830 - 75,238,021 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,442,005 - 75,445,196NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,518,128 - 68,521,319 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. [Beta-defensins in plasma and bronchoalveolar lavage fluid in patients with non-tuberculous mycobacterium infection]. Ashitani J, etal., Nihon Kokyuki Gakkai Zasshi. 2001 Jan;39(1):12-6.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. [A study of human beta-defensin-1 and human beta-defensin-2 in airway mucosal defense]. Hiratsuka T, etal., Kansenshogaku Zasshi. 1999 Feb;73(2):156-62.
4. Molecular cloning and characterization of rat genes encoding homologues of human beta-defensins. Jia HP, etal., Infect Immun 1999 Sep;67(9):4827-33.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Elevated BALF concentrations of alpha- and beta-defensins in patients with pulmonary alveolar proteinosis. Mukae H, etal., Respir Med. 2007 Apr;101(4):715-21. Epub 2006 Sep 26.
7. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
8. Human rhinovirus infection induces airway epithelial cell production of human beta-defensin 2 both in vitro and in vivo. Proud D, etal., J Immunol. 2004 Apr 1;172(7):4637-45.
9. GOA pipeline RGD automated data pipeline
10. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
11. Comprehensive gene review and curation RGD comprehensive gene curation
12. Increased levels of antimicrobial peptides in tracheal aspirates of newborn infants during infection. Schaller-Bals S, etal., Am J Respir Crit Care Med. 2002 Apr 1;165(7):992-5.
13. Production of beta-defensins by human airway epithelia. Singh PK, etal., Proc Natl Acad Sci U S A. 1998 Dec 8;95(25):14961-6.
14. [Effect of recombinant beta-defensin-2 peptide on apoptosis of pulmonary tissue in rats with sepsis]. Xu XY, etal., Zhejiang Da Xue Xue Bao Yi Xue Ban. 2006 Nov;35(6):600-4.
Additional References at PubMed
PMID:9727055   PMID:12533413   PMID:15625724   PMID:16033865   PMID:19109182   PMID:20068036   PMID:20150208   PMID:21115716   PMID:21518253   PMID:23670560  


Genomics

Comparative Map Data
Defb4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,352,911 - 77,356,104 (-)NCBIGRCr8
mRatBN7.21670,650,472 - 70,653,665 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,650,472 - 70,653,665 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,927,305 - 75,930,496 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,390,193 - 79,393,646 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,639,631 - 74,643,084 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,634,598 - 75,637,789 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,634,598 - 75,637,789 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,234,830 - 75,238,021 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,442,005 - 75,445,196NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,518,128 - 68,521,319 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFB4B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3887,414,855 - 7,416,863 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl87,414,855 - 7,416,863 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl87,894,677 - 7,896,716 (+)EnsemblGRCh38hg38GRCh38
GRCh3787,272,377 - 7,274,385 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3687,259,788 - 7,261,795 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map8p23.1NCBI
CHM1_187,353,453 - 7,355,430 (+)NCBICHM1_1
T2T-CHM13v2.087,143,841 - 7,145,853 (-)NCBIT2T-CHM13v2.0
Defb7
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39819,545,113 - 19,547,791 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl819,545,113 - 19,547,791 (+)EnsemblGRCm39 Ensembl
GRCm38819,495,097 - 19,497,775 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl819,495,097 - 19,497,775 (+)EnsemblGRCm38mm10GRCm38
MGSCv37819,495,097 - 19,497,775 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36819,495,074 - 19,497,752 (+)NCBIMGSCv36mm8
Celera819,659,779 - 19,662,429 (+)NCBICelera
Cytogenetic Map8A1.3NCBI
cM Map810.35NCBI
LOC103215308
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.186,882,136 - 6,886,527 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605235,560,415 - 35,563,342 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Defb4
160 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:16
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000058029
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)166853271675029966Rat

Markers in Region
PMC96815P2  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,650,488 - 70,650,666 (+)MAPPERmRatBN7.2
Rnor_6.01675,634,615 - 75,634,792NCBIRnor6.0
Rnor_5.01675,234,847 - 75,235,024UniSTSRnor5.0
RGSC_v3.41675,442,022 - 75,442,199UniSTSRGSC3.4
Celera1668,518,145 - 68,518,322UniSTS
Cytogenetic Map16q12.5UniSTS


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2
Medium 9
Low 9 4 5 4 4 4 1 8 4
Below cutoff 8 9 3 8 3 4 4 13 5 10 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058029   ⟹   ENSRNOP00000054838
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,650,472 - 70,653,665 (-)Ensembl
Rnor_6.0 Ensembl1675,634,598 - 75,637,789 (-)Ensembl
RefSeq Acc Id: NM_022544   ⟹   NP_071989
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,352,911 - 77,356,104 (-)NCBI
mRatBN7.21670,650,472 - 70,653,665 (-)NCBI
Rnor_6.01675,634,598 - 75,637,789 (-)NCBI
Rnor_5.01675,234,830 - 75,238,021 (-)NCBI
RGSC_v3.41675,442,005 - 75,445,196 (-)RGD
Celera1668,518,128 - 68,521,319 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_071989 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAC28072 (Get FASTA)   NCBI Sequence Viewer  
  AAT51913 (Get FASTA)   NCBI Sequence Viewer  
  EDM08969 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054838
  ENSRNOP00000054838.1
  ENSRNOP00055011526
  ENSRNOP00060025119
  ENSRNOP00065010344
GenBank Protein O88514 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_071989   ⟸   NM_022544
- Peptide Label: precursor
- UniProtKB: Q32ZE9 (UniProtKB/Swiss-Prot),   O88514 (UniProtKB/Swiss-Prot),   A6IWA3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054838   ⟸   ENSRNOT00000058029

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O88514-F1-model_v2 AlphaFold O88514 1-63 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13700212
Promoter ID:EPDNEW_R10736
Type:single initiation site
Name:Defb4_1
Description:defensin beta 4
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01675,637,680 - 75,637,740EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:619944 AgrOrtholog
BioCyc Gene G2FUF-10820 BioCyc
Ensembl Genes ENSRNOG00000013939 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055008533 UniProtKB/Swiss-Prot
  ENSRNOG00060018093 UniProtKB/Swiss-Prot
  ENSRNOG00065008731 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000058029 ENTREZGENE
  ENSRNOT00000058029.2 UniProtKB/Swiss-Prot
  ENSRNOT00055014398 UniProtKB/Swiss-Prot
  ENSRNOT00060031014 UniProtKB/Swiss-Prot
  ENSRNOT00065013897 UniProtKB/Swiss-Prot
InterPro Defensin_beta-typ UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:64389 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 64389 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BETA-DEFENSIN 4A UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Defensin_beta UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Defb4 PhenoGen
RatGTEx ENSRNOG00000013939 RatGTEx
  ENSRNOG00055008533 RatGTEx
  ENSRNOG00060018093 RatGTEx
  ENSRNOG00065008731 RatGTEx
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6IWA3 ENTREZGENE, UniProtKB/TrEMBL
  DEFB4_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q32ZE9 ENTREZGENE
UniProt Secondary Q32ZE9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb4  defensin beta 4  Defb3  defensin beta 3  Symbol and Name updated 1299863 APPROVED
2004-09-10 Defb3  defensin beta 3  Defb2  beta defensin-2  Symbol and Name updated 1299863 APPROVED
2002-08-07 Defb2  beta defensin-2      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression ubiquitously expressed; abundant in lung 727279
gene_protein 63 amino acids 727279