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
RGD ID: 727857
Description: Predicted to enable protein homodimerization activity. Predicted to be involved in several processes, including T cell chemotaxis; cellular response to lipopolysaccharide; and defense response to other organism. Predicted to act upstream of or within defense response to bacterium. Predicted to be located in azurophil granule. Predicted to be active in extracellular space. 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
Mouse
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,494,607 - 70,497,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,529 - 70,497,202 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,771,469 - 75,774,026 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01679,217,054 - 79,219,596 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01674,466,481 - 74,469,025 (-)NCBIRnor_WKY
Rnor_6.01675,478,548 - 75,481,146 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,414,786 - 75,481,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,079,890 - 75,082,489 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,284,693 - 75,337,014 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11675,284,957 - 75,337,279 (-)NCBI
Celera1668,357,038 - 68,359,592 (-)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. 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
mRatBN7.21670,494,607 - 70,497,261 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,529 - 70,497,202 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,771,469 - 75,774,026 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01679,217,054 - 79,219,596 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01674,466,481 - 74,469,025 (-)NCBIRnor_WKY
Rnor_6.01675,478,548 - 75,481,146 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,414,786 - 75,481,115 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,079,890 - 75,082,489 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,284,693 - 75,337,014 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11675,284,957 - 75,337,279 (-)NCBI
Celera1668,357,038 - 68,359,592 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFA4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3886,935,820 - 6,938,306 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl86,935,820 - 6,938,306 (-)EnsemblGRCh38hg38GRCh38
GRCh3786,793,342 - 6,795,828 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3686,780,755 - 6,783,196 (-)NCBINCBI36Build 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
Defa31
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39821,681,589 - 21,682,566 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl821,681,630 - 21,682,565 (+)EnsemblGRCm39 Ensembl
GRCm38821,191,573 - 21,192,550 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl821,191,614 - 21,192,549 (+)EnsemblGRCm38mm10GRCm38
MGSCv37822,331,252 - 22,332,229 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36822,686,366 - 22,686,536 (+)NCBIMGSCv36mm8
Celera820,990,359 - 20,991,328 (-)NCBICelera
Cytogenetic Map8A2NCBI
DEFA4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.186,938,152 - 6,940,669 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl86,938,152 - 6,940,669 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v08344,350 - 346,835 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
DEFA4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_02366605448,826,975 - 48,836,477 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Np4
17 total Variants
miRNA Target Status

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 (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
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
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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 23 18 13 18
Low 1 7 11 7 6 7 1 2 13 17 1
Below cutoff 1 12 7 5 5 5 6 24 11 11 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029297   ⟹   ENSRNOP00000037267
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,419,277 - 70,420,046 (-)Ensembl
Rnor_6.0 Ensembl1675,414,786 - 75,415,555 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000035128   ⟹   ENSRNOP00000036962
RefSeq Status:
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
RefSeq Acc Id: ENSRNOT00000088257   ⟹   ENSRNOP00000072461
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1675,414,786 - 75,479,492 (-)Ensembl
RefSeq Acc Id: NM_173299   ⟹   NP_775421
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21670,494,613 - 70,497,170 (-)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
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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  
  Q62714 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
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
- UniProtKB: A0A8L2QLB0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000037267   ⟸   ENSRNOT00000029297
RefSeq Acc Id: ENSRNOP00000036962   ⟸   ENSRNOT00000035128
RefSeq Acc Id: ENSRNOP00000072461   ⟸   ENSRNOT00000088257
Protein Domains
DEFENSIN

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, UniProtKB/TrEMBL
  ENSRNOG00000069755 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000036962 ENTREZGENE
  ENSRNOP00000036962.3 UniProtKB/TrEMBL
  ENSRNOP00000037267.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000029297.4 UniProtKB/TrEMBL
  ENSRNOT00000035128 ENTREZGENE
  ENSRNOT00000035128.5 UniProtKB/TrEMBL
InterPro Alpha-defensin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Alpha-defensin_pro UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Defensin_beta/alpha UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Defensin_propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:286958 UniProtKB/Swiss-Prot
NCBI Gene 286958 ENTREZGENE
PANTHER PTHR11876 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Defensin_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Defensin_propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Np4 PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DEFENSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEFSN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8L2QLB0 ENTREZGENE, UniProtKB/TrEMBL
  DEF4_RAT UniProtKB/Swiss-Prot
  F1LQB7_RAT UniProtKB/TrEMBL
  Q62714 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