Ratnp-3b (defensin rat NP-3 precursor) - 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 Behavioral & Substance Use Disorder 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 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
Advanced Search (OLGA)
Gene: Ratnp-3b (defensin rat NP-3 precursor) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ratnp-3b
Name: defensin rat NP-3 precursor (Ensembl:defensin RatNP-3 precursor)
RGD ID: 1589653
Description: Predicted to be involved in defense response to bacterium; defense response to fungus; and killing of cells of another organism. Predicted to be located in extracellular space. Orthologous to several human genes including DEFA5 (defensin alpha 5); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: defensin 3a; defensin 3b; defensin NP-3; defensin RatNP-3; defensin RatNP-3 precursor; neutrophil antibiotic peptide NP-3; Neutrophil antibiotic peptide NP-3A; neutrophil antibiotic peptide NP-3B; neutrophil defensin 3; NP-3; NP-3a; NP-3b; Np3; ratNP-3a
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,246,811 - 77,248,977 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,216,342 - 77,248,966 (-)EnsemblGRCr8
mRatBN7.21670,544,364 - 70,546,533 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,513,888 - 70,546,522 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,821,206 - 75,823,366 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,266,694 - 79,268,858 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,516,135 - 74,518,299 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,528,348 - 75,530,511 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,497,832 - 75,530,517 (-)Ensemblrn6Rnor6.0
Rnor_5.01675,129,190 - 75,131,353 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,334,851 - 75,337,014 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,406,110 - 68,408,276 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

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. 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:2543629   PMID:7594610  


Genomics

Variants

.
Variants in Ratnp-3b
11 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:9
Count of miRNA genes:9
Interacting mature miRNAs:9
Transcripts:ENSRNOT00000018580
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)167523528581732231Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat

Markers in Region
D16Wox28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,545,338 - 70,545,538 (+)MAPPERmRatBN7.2
Rnor_6.01675,529,317 - 75,529,516NCBIRnor6.0
Rnor_5.01675,130,159 - 75,130,358UniSTSRnor5.0
RGSC_v3.41675,335,820 - 75,336,019UniSTSRGSC3.4
Celera1668,407,079 - 68,407,278UniSTS
Cytogenetic Map16q12.5UniSTS
PMC96815P3  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr81677,246,854 - 77,247,032 (+)Marker Load Pipeline
Rnor_6.01675,528,392 - 75,528,566NCBIRnor6.0
Rnor_5.01675,129,234 - 75,129,408UniSTSRnor5.0
RGSC_v3.41675,334,895 - 75,335,069UniSTSRGSC3.4
Celera1668,406,154 - 68,406,328UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 36 104 78 78 49 32 49 4 199 95 11 78 31 49 29 2 2

Sequence


Ensembl Acc Id: ENSRNOT00000018580   ⟹   ENSRNOP00000018580
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,513,888 - 70,546,522 (-)Ensembl
Rnor_6.0 Ensembl1675,497,832 - 75,530,500 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000086035   ⟹   ENSRNOP00000071526
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1675,528,348 - 75,530,517 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120639   ⟹   ENSRNOP00000098274
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,216,342 - 77,248,966 (-)Ensembl
RefSeq Acc Id: NM_001079898   ⟹   NP_001073367
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,246,811 - 77,248,977 (-)NCBI
mRatBN7.21670,544,364 - 70,546,533 (-)NCBI
Rnor_6.01675,528,348 - 75,530,511 (-)NCBI
Rnor_5.01675,129,190 - 75,131,353 (-)NCBI
RGSC_v3.41675,334,851 - 75,337,014 (-)RGD
Celera1668,406,110 - 68,408,276 (-)RGD
Sequence:
RefSeq Acc Id: NP_001073367   ⟸   NM_001079898
- Peptide Label: precursor
- UniProtKB: Q62713 (UniProtKB/Swiss-Prot),   Q9Z1F1 (UniProtKB/Swiss-Prot),   A6IWA0 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018580   ⟸   ENSRNOT00000018580
Ensembl Acc Id: ENSRNOP00000071526   ⟸   ENSRNOT00000086035
Ensembl Acc Id: ENSRNOP00000098274   ⟸   ENSRNOT00000120639
Protein Domains
Mammalian defensins

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62713-F1-model_v2 AlphaFold Q62713 1-87 view protein structure
AF-Q9Z1F1-F1-model_v2 AlphaFold Q9Z1F1 1-87 view protein structure

Transcriptome

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

Promoters
RGD ID:13700209
Promoter ID:EPDNEW_R10733
Type:single initiation site
Name:RatNP-3b_1
Description:defensin RatNP-3 precursor
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_6.01675,530,529 - 75,530,589EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1589653 AgrOrtholog
BioCyc Gene G2FUF-10825 BioCyc
Ensembl Genes ENSRNOG00000038135 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018580.8 UniProtKB/Swiss-Prot
  ENSRNOT00000120639 ENTREZGENE
InterPro Alpha-defensin UniProtKB/Swiss-Prot
  Alpha-defensin_pro UniProtKB/Swiss-Prot
  Defensin_beta/alpha UniProtKB/Swiss-Prot
  Defensin_propep UniProtKB/Swiss-Prot
KEGG Report rno:498659 UniProtKB/Swiss-Prot
NCBI Gene 498659 ENTREZGENE
PANTHER DEFENSIN ALPHA 10-RELATED UniProtKB/Swiss-Prot
  PTHR11876 UniProtKB/Swiss-Prot
Pfam Defensin_1 UniProtKB/Swiss-Prot
  Defensin_propep UniProtKB/Swiss-Prot
PhenoGen Ratnp-3b PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot
PROSITE DEFENSIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000038135 RatGTEx
SMART Defensin_propep UniProtKB/Swiss-Prot
  DEFSN UniProtKB/Swiss-Prot
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot
UniProt A6IWA0 ENTREZGENE, UniProtKB/TrEMBL
  DEF3A_RAT UniProtKB/Swiss-Prot
  DEF3B_RAT UniProtKB/Swiss-Prot
  Q62713 ENTREZGENE
  Q9Z1F1 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2025-02-04 Ratnp-3b  defensin rat NP-3 precursor  RatNP-3b  defensin RatNP-3 precursor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 RatNP-3b  defensin RatNP-3 precursor      Symbol and Name status set to provisional 70820 PROVISIONAL