Np4 (defensin NP-4 precursor) - Rat Genome Database

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Gene: Np4 (defensin NP-4 precursor) Rattus norvegicus
Analyze
Symbol: Np4
Name: defensin NP-4 precursor (Ensembl:defensin NP-4)
RGD ID: 727857
Description: Predicted to enable pore-forming activity and protein homodimerization activity. Predicted to be involved in several processes, including T cell chemotaxis; defense response to bacterium; and defense response to symbiont. Predicted to be located in azurophil granule. Predicted to be active in extracellular region. Orthologous to several human genes including DEFA5 (defensin alpha 5); INTERACTS WITH 17beta-estradiol; 17beta-estradiol 3-benzoate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: defensin 3b; defensin alpha 4; neutrophil antibiotic peptide NP-4; neutrophil defensin 4; NP-4; ratNP-4
RGD Orthologs
Human
Bonobo
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,197,061 - 77,199,713 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,197,065 - 77,199,642 (-)EnsemblGRCr8
GRCr8 Ensembl1677,121,639 - 77,122,502 (-)EnsemblGRCr8
mRatBN7.21670,494,607 - 70,497,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,529 - 70,497,202 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,771,469 - 75,774,026 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,217,054 - 79,219,596 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,466,481 - 74,469,025 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1677,145,146 - 77,147,711 (-)NCBI
Lyon_Normotensive1678,518,251 - 78,520,816 (-)NCBI
Lyon_Hypertensive1679,019,242 - 79,021,807 (-)NCBI
F344_StmMcwi1675,181,105 - 75,183,679 (-)NCBI
Rnor_6.01675,478,548 - 75,481,146 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,414,786 - 75,481,115 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.01675,079,890 - 75,082,489 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,284,693 - 75,337,014 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,357,038 - 68,359,592 (-)NCBICelera
RGSC_v3.11675,284,957 - 75,337,279 (-)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




Disease 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. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Rat neutrophil defensins. Precursor structures and expression during neutrophilic myelopoiesis. Yount NY, etal., J Immunol 1995 Nov 1;155(9):4476-84.
Additional References at PubMed
PMID:2500436   PMID:2543629   PMID:15235601   PMID:15616305   PMID:17088326  


Genomics

Comparative Map Data
Np4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,197,061 - 77,199,713 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,197,065 - 77,199,642 (-)EnsemblGRCr8
GRCr8 Ensembl1677,121,639 - 77,122,502 (-)EnsemblGRCr8
mRatBN7.21670,494,607 - 70,497,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,529 - 70,497,202 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,771,469 - 75,774,026 (-)NCBIUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,217,054 - 79,219,596 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,466,481 - 74,469,025 (-)NCBIUTH_Rnor_WKY_Bbb_1.0
Dahl_SR_JrHsd1677,145,146 - 77,147,711 (-)NCBI
Lyon_Normotensive1678,518,251 - 78,520,816 (-)NCBI
Lyon_Hypertensive1679,019,242 - 79,021,807 (-)NCBI
F344_StmMcwi1675,181,105 - 75,183,679 (-)NCBI
Rnor_6.01675,478,548 - 75,481,146 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,414,786 - 75,481,115 (-)EnsemblRnor_6.0 Ensemblrn6Rnor6.0
Rnor_5.01675,079,890 - 75,082,489 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,284,693 - 75,337,014 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,357,038 - 68,359,592 (-)NCBICelera
RGSC_v3.11675,284,957 - 75,337,279 (-)NCBI
Cytogenetic Map16q12.5NCBI
DEFA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3886,935,820 - 6,938,306 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl86,935,820 - 6,938,313 (-)EnsemblGRCh38.p14 Ensemblhg38GRCh38
GRCh3786,793,342 - 6,795,828 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3686,780,755 - 6,783,196 (-)NCBIBuild 36Build 36hg18NCBI36
Build 3486,780,754 - 6,783,196NCBI
Celera86,770,132 - 6,772,573 (-)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef86,572,881 - 6,575,322 (-)NCBIHuRef
CHM1_186,882,470 - 6,884,911 (-)NCBICHM1_1
T2T-CHM13v2.086,690,512 - 6,692,998 (-)NCBIT2T-CHM13v2.0
DEFA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2721,738,846 - 21,741,331 (-)NCBINHGRI_mPanPan1-v2
Mhudiblu_PPA_v08344,350 - 346,835 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.186,938,152 - 6,940,669 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl86,938,152 - 6,940,669 (-)EnsemblPanPan1.1 EnsemblpanPan2panpan1.1
DEFA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mChlSab1.0.hap187,744,300 - 7,762,396 (-)NCBImChlSab1.0.hap1
Vero_WHO_p1.0NW_02366605448,826,975 - 48,836,477 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Np4
13 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:44
Count of miRNA genes:24
Interacting mature miRNAs:24
Transcripts:ENSRNOT00000035128, ENSRNOT00000058039
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
D16Wox27  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,495,550 - 70,495,732 (+)MAPPERmRatBN7.2
Rnor_6.01675,479,492 - 75,479,673NCBIRnor6.0
Rnor_5.01675,080,834 - 75,081,015UniSTSRnor5.0
RGSC_v3.41675,285,631 - 75,285,812UniSTSRGSC3.4
Celera1668,357,973 - 68,358,154UniSTS
Cytogenetic Map16q12.5UniSTS
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
PMC96815P4  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21670,494,661 - 70,494,784 (+)MAPPERmRatBN7.2
Rnor_6.01675,478,603 - 75,478,725NCBIRnor6.0
Rnor_5.01675,079,945 - 75,080,067UniSTSRnor5.0
RGSC_v3.41675,284,742 - 75,284,864UniSTSRGSC3.4
Celera1668,357,087 - 68,357,209UniSTS
Cytogenetic Map16q12.5UniSTS


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
pharyngeal arch
renal system
reproductive system
respiratory system
sensory system
visual system
20 9 114 165 952 309 656 35 248 333 237 12 1249 686 407 937 11 200 225 431 8 7

Sequence


Ensembl Acc Id: ENSRNOT00000029297   ⟹   ENSRNOP00000037267
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,121,639 - 77,122,502 (-)Ensembl
mRatBN7.2 Ensembl1670,419,277 - 70,420,046 (-)Ensembl
Rnor_6.0 Ensembl1675,414,786 - 75,415,555 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000035128   ⟹   ENSRNOP00000036962
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,342,529 - 70,497,202 (-)Ensembl
Rnor_6.0 Ensembl1675,478,549 - 75,481,115 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000088257   ⟹   ENSRNOP00000072461
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1675,414,786 - 75,479,492 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000120638   ⟹   ENSRNOP00000098273
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,197,065 - 77,199,642 (-)Ensembl
RefSeq Acc Id: NM_173299   ⟹   NP_775421
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,197,065 - 77,199,642 (-)NCBI
mRatBN7.21670,494,611 - 70,497,188 (-)NCBI
Dahl_SR_JrHsd1677,145,146 - 77,147,711 (-)NCBI
Lyon_Normotensive1678,518,251 - 78,520,816 (-)NCBI
Lyon_Hypertensive1679,019,242 - 79,021,807 (-)NCBI
F344_StmMcwi1675,181,105 - 75,183,679 (-)NCBI
Rnor_6.01675,478,554 - 75,481,111 (-)NCBI
Rnor_5.01675,079,890 - 75,082,489 (-)NCBI
RGSC_v3.41675,284,693 - 75,337,014 (-)RGD
Celera1668,357,038 - 68,359,592 (-)RGD
Sequence:
RefSeq Acc Id: XM_006253366   ⟹   XP_006253428
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,197,061 - 77,199,713 (-)NCBI
mRatBN7.21670,494,607 - 70,497,261 (-)NCBI
Rnor_6.01675,478,548 - 75,481,146 (-)NCBI
Rnor_5.01675,079,890 - 75,082,489 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_775421 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253428 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA91972 (Get FASTA)   NCBI Sequence Viewer  
  AAC99552 (Get FASTA)   NCBI Sequence Viewer  
  EDM08973 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000098273
  ENSRNOP00000098273.1
GenBank Protein Q62714 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_775421   ⟸   NM_173299
- Peptide Label: precursor
- UniProtKB: Q62714 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006253428   ⟸   XM_006253366
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000037267   ⟸   ENSRNOT00000029297
Ensembl Acc Id: ENSRNOP00000036962   ⟸   ENSRNOT00000035128
Ensembl Acc Id: ENSRNOP00000072461   ⟸   ENSRNOT00000088257
Ensembl Acc Id: ENSRNOP00000098273   ⟸   ENSRNOT00000120638

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62714-F1-model_v2 AlphaFold Q62714 1-93 view protein structure

Transcriptome

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

Promoters
RGD ID:13700208
Promoter ID:EPDNEW_R10732
Type:single initiation site
Name:Np4_1
Description:defensin NP-4 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_6.01675,481,129 - 75,481,189EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727857 AgrOrtholog
BioCyc Gene G2FUF-10828 BioCyc
Ensembl Genes ENSRNOG00000028707 Ensembl
  ENSRNOG00000069755 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000120638 ENTREZGENE
  ENSRNOT00000120638.2 UniProtKB/Swiss-Prot
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:286958 UniProtKB/Swiss-Prot
NCBI Gene 286958 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 Np4 PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot
PROSITE DEFENSIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000028707 RatGTEx
  ENSRNOG00000069755 RatGTEx
SMART Defensin_propep UniProtKB/Swiss-Prot
  DEFSN UniProtKB/Swiss-Prot
Superfamily-SCOP Defensin-like UniProtKB/Swiss-Prot
UniProt DEF4_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-07-08 Np4  defensin NP-4 precursor      Symbol and Name status set to approved 1299863 APPROVED