Defb3 (beta-defensin 3) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Defb3 (beta-defensin 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defb3
Name: beta-defensin 3
RGD ID: 1589572
Description: Predicted to enable CCR6 chemokine receptor binding activity and chemoattractant activity. Predicted to be involved in cell chemotaxis and defense response to bacterium. Predicted to be active in extracellular space. Orthologous to human DEFB4A (defensin beta 4A) and DEFB4B (defensin beta 4B).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: BD-3; defensin, beta 3
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
NCBI Annotation Information: Genome Annotation Status: not in current annotation release
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
UTH_Rnor_SHRSP_BbbUtx_1.01679,329,290 - 79,339,270 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,578,730 - 74,588,708 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0 Ensembl1675,589,530 - 75,599,534 (-)EnsemblRnor6.0rn6Rnor6.0
RGSC_v3.41675,395,318 - 75,405,271 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,467,683 - 68,477,637 (-)NCBICelera
Cytogenetic Map16q12.4-q12.5NCBI


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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:20068036   PMID:21115716   PMID:21442129  


Genomics

Markers in Region
D16Rat14  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,610,849 - 70,610,983 (+)MAPPERmRatBN7.2
Rnor_6.01675,594,973 - 75,595,106NCBIRnor6.0
Rnor_5.01675,195,671 - 75,195,804UniSTSRnor5.0
RGSC_v3.41675,400,761 - 75,400,894UniSTSRGSC3.4
RGSC_v3.41675,400,760 - 75,400,894RGDRGSC3.4
RGSC_v3.11675,401,025 - 75,401,159RGD
Celera1668,473,126 - 68,473,259UniSTS
RH 3.4 Map16694.4RGD
RH 3.4 Map16694.4UniSTS
RH 2.0 Map16801.6RGD
SHRSP x BN Map1638.59RGD
FHH x ACI Map1640.2499RGD
Cytogenetic Map16q12.4-q12.5UniSTS


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

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

Nucleotide Sequences
RefSeq Transcripts NM_001037548 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000018653   ⟹   ENSRNOP00000018655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,613,146 - 70,615,467 (-)Ensembl
Rnor_6.0 Ensembl1675,597,224 - 75,599,534 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000058030   ⟹   ENSRNOP00000054839
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1675,589,530 - 75,599,483 (-)Ensembl
RefSeq Acc Id: NM_001037548   ⟹   NP_001032637
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
RGSC_v3.41675,395,318 - 75,405,271 (-)RGD
Celera1668,467,683 - 68,477,637 (-)RGD
Protein Sequences
Protein RefSeqs NP_001032637 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein Q32ZI4 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001032637   ⟸   NM_001037548
- Peptide Label: precursor
- UniProtKB: Q32ZI4 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSRNOP00000018655   ⟸   ENSRNOT00000018653
RefSeq Acc Id: ENSRNOP00000054839   ⟸   ENSRNOT00000058030

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZI4-F1-model_v2 AlphaFold Q32ZI4 1-63 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589572 AgrOrtholog
Ensembl Genes ENSRNOG00000038126 Ensembl
InterPro Defensin_beta-typ UniProtKB/Swiss-Prot
NCBI Gene 641623 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/Swiss-Prot
  BETA-DEFENSIN 3-RELATED UniProtKB/Swiss-Prot
Pfam Defensin_beta UniProtKB/Swiss-Prot
PhenoGen Defb3 PhenoGen
RatGTEx ENSRNOG00000038126 RatGTEx
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot
UniProt DEFB3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-19 Defb3  beta-defensin 3      Symbol and Name status set to provisional 70820 PROVISIONAL