Defb5 (defensin beta 5) - Rat Genome Database

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Pathways
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Gene: Defb5 (defensin beta 5) Rattus norvegicus
Analyze
Symbol: Defb5
Name: defensin beta 5
RGD ID: 1563630
Description: Predicted to enable CCR6 chemokine receptor binding activity; chemoattractant activity; and phosphatidylinositol-4,5-bisphosphate binding activity. Predicted to be involved in cell chemotaxis and defense response to other organism. Predicted to be active in extracellular space. Orthologous to human DEFB4B (defensin beta 4B); INTERACTS WITH all-trans-retinoic acid; ammonium chloride; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BD-5; beta-defensin 5; defensin, beta 5
RGD Orthologs
Human
Mouse
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,315,424 - 77,317,828 (-)NCBIGRCr8
mRatBN7.21670,612,985 - 70,615,389 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,613,146 - 70,615,467 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,890,029 - 75,892,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,345,916 - 79,367,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,595,354 - 74,616,645 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,597,323 - 75,599,483 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,589,530 - 75,599,534 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,190,208 - 75,200,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,403,111 - 75,405,271 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,475,476 - 68,477,637 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:9727055   PMID:15625724   PMID:16033865   PMID:19109182   PMID:20068036   PMID:21115716  


Genomics

Comparative Map Data
Defb5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,315,424 - 77,317,828 (-)NCBIGRCr8
mRatBN7.21670,612,985 - 70,615,389 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,613,146 - 70,615,467 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,890,029 - 75,892,189 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,345,916 - 79,367,209 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,595,354 - 74,616,645 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,597,323 - 75,599,483 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,589,530 - 75,599,534 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,190,208 - 75,200,200 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,403,111 - 75,405,271 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,475,476 - 68,477,637 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFB4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3887,894,677 - 7,896,716 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl87,894,677 - 7,896,716 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl87,414,855 - 7,416,863 (-)EnsemblGRCh38hg38GRCh38
GRCh3787,752,199 - 7,754,238 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3687,789,609 - 7,791,647 (+)NCBINCBI36Build 36hg18NCBI36
Build 3487,789,608 - 7,791,647NCBI
Cytogenetic Map8p23.1NCBI
CHM1_187,817,857 - 7,819,910 (+)NCBICHM1_1
T2T-CHM13v2.0812,040,687 - 12,042,691 (+)NCBIT2T-CHM13v2.0
Defb4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39819,248,720 - 19,251,563 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl819,248,722 - 19,251,561 (+)EnsemblGRCm39 Ensembl
GRCm38819,198,704 - 19,201,547 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl819,198,706 - 19,201,545 (+)EnsemblGRCm38mm10GRCm38
MGSCv37819,198,704 - 19,201,547 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36819,198,683 - 19,201,522 (+)NCBIMGSCv36mm8
Celera819,322,586 - 19,325,383 (+)NCBICelera
Cytogenetic Map8A1.3NCBI
cM Map810.35NCBI

Variants

.
Variants in Defb5
213 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:95
Interacting mature miRNAs:97
Transcripts:ENSRNOT00000018653, ENSRNOT00000058030
Prediction methods:Microtar, 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


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

endocrine system exocrine system hemolymphoid system hepatobiliary system nervous system reproductive system respiratory system
High
Medium 1
Low 4 3
Below cutoff 3 2 1 2 1 2 5

Sequence


Reference Sequences
RefSeq Acc Id: NM_001037549   ⟹   NP_001032638
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,315,424 - 77,317,828 (-)NCBI
mRatBN7.21670,612,985 - 70,615,389 (-)NCBI
Rnor_6.01675,597,323 - 75,599,483 (-)NCBI
Rnor_5.01675,190,208 - 75,200,200 (-)NCBI
RGSC_v3.41675,403,111 - 75,405,271 (-)RGD
Celera1668,475,476 - 68,477,637 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032638 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51878 (Get FASTA)   NCBI Sequence Viewer  
  AAT51879 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018655
  ENSRNOP00000018655.3
  ENSRNOP00060039957
GenBank Protein Q32ZI3 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001032638   ⟸   NM_001037549
- Peptide Label: precursor
- UniProtKB: Q32ZI3 (UniProtKB/Swiss-Prot)
- Sequence:

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZI3-F1-model_v2 AlphaFold Q32ZI3 1-63 view protein structure

Transcriptome

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

Promoters
RGD ID:13700230
Promoter ID:EPDNEW_R10735
Type:single initiation site
Name:Defb5_1
Description:defensin beta 5
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_6.01675,599,510 - 75,599,570EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563630 AgrOrtholog
BioCyc Gene G2FUF-10821 BioCyc
Ensembl Genes ENSRNOG00000038126 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00060027676 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018653 ENTREZGENE
  ENSRNOT00000018653.6 UniProtKB/Swiss-Prot
  ENSRNOT00060048013 UniProtKB/Swiss-Prot
InterPro Defensin_beta-typ UniProtKB/Swiss-Prot
KEGG Report rno:641624 UniProtKB/Swiss-Prot
NCBI Gene 641624 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/Swiss-Prot
  BETA-DEFENSIN 4A UniProtKB/Swiss-Prot
Pfam Defensin_beta UniProtKB/Swiss-Prot
PhenoGen Defb5 PhenoGen
RatGTEx ENSRNOG00000038126 RatGTEx
  ENSRNOG00060027676 RatGTEx
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot
UniProt DEFB5_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb5  defensin beta 5    beta-defensin 5  Name updated 1299863 APPROVED
2006-02-09 Defb5  beta-defensin 5      Symbol and Name status set to provisional 70820 PROVISIONAL