Defa5 (defensin alpha 5) - Rat Genome Database

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Gene: Defa5 (defensin alpha 5) Rattus norvegicus
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Symbol: Defa5
Name: defensin alpha 5
RGD ID: 727951
Description: Predicted to enable protein homodimerization activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of interleukin-8 production; and protein homotetramerization. Predicted to be located in midbody and secretory 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; acetylsalicylic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-defensin 5, Paneth cell-specific; Defa; defensin NP-2; defensin NP-2 precursor; defensin, alpha 5, Paneth cell-specific; LOC286995; neutrophil antibiotic peptide NP-1; neutrophil antibiotic peptide NP-2; neutrophil defensin 1; neutrophil defensin 2; ratNP-1; ratNP-2
RGD Orthologs
Human
Mouse
Bonobo
Green Monkey
Alliance Genes
More Info more info ...
Related Pseudogenes: Defa5-ps2  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,342,530 - 70,344,836 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,530 - 70,344,836 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,616,245 - 75,618,551 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01679,069,107 - 79,071,419 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01674,318,539 - 74,320,851 (-)NCBIRnor_WKY
Rnor_6.01675,338,050 - 75,340,401 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,338,052 - 75,340,360 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,952,566 - 74,954,917 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,024,375 - 75,026,675 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11675,024,639 - 75,026,940 (-)NCBI
Celera1668,215,238 - 68,217,544 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
3. NCBI rat LocusLink and RefSeq merged data October 15, 2003 NCBI rat LocusLink and RefSeq merged data October 15, 2003
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. 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:2254017   PMID:2543629   PMID:9169780   PMID:15616305   PMID:17088326   PMID:21861459   PMID:30480410  


Genomics

Comparative Map Data
Defa5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,342,530 - 70,344,836 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,342,530 - 70,344,836 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,616,245 - 75,618,551 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01679,069,107 - 79,071,419 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01674,318,539 - 74,320,851 (-)NCBIRnor_WKY
Rnor_6.01675,338,050 - 75,340,401 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,338,052 - 75,340,360 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,952,566 - 74,954,917 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,024,375 - 75,026,675 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11675,024,639 - 75,026,940 (-)NCBI
Celera1668,215,238 - 68,217,544 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3887,055,304 - 7,056,739 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl87,055,304 - 7,056,739 (-)EnsemblGRCh38hg38GRCh38
GRCh3786,912,826 - 6,914,261 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3686,900,239 - 6,901,669 (-)NCBINCBI36Build 36hg18NCBI36
Build 3486,900,238 - 6,901,669NCBI
Celera86,879,990 - 6,881,416 (-)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef86,654,020 - 6,655,446 (-)NCBIHuRef
CHM1_187,001,371 - 7,002,801 (-)NCBICHM1_1
T2T-CHM13v2.086,809,926 - 6,811,358 (-)NCBIT2T-CHM13v2.0
Defa21
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39821,515,561 - 21,516,533 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl821,515,561 - 21,516,532 (+)EnsemblGRCm39 Ensembl
GRCm38821,025,545 - 21,026,517 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl821,025,545 - 21,026,516 (+)EnsemblGRCm38mm10GRCm38
MGSCv37822,165,224 - 22,166,196 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36822,520,296 - 22,521,268 (+)NCBIMGSCv36mm8
Celera822,918,740 - 22,919,712 (+)NCBICelera
Cytogenetic Map8A2NCBI
LOC100991118
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Mhudiblu_PPA_v08264,298 - 265,962 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
DEFA5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Vero_WHO_p1.0NW_023669959743 - 2,256 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Defa5
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:9
Count of miRNA genes:9
Interacting mature miRNAs:9
Transcripts:ENSRNOT00000018501
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 diameter (CMO:0001889)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
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

circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High 2 2 2
Medium 24 18 13 18
Low 6 9 5 6 5 1 1 5 12 15 1
Below cutoff 13 10 7 7 3 3 17 7 8 4 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018501   ⟹   ENSRNOP00000018501
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,342,530 - 70,344,836 (-)Ensembl
Rnor_6.0 Ensembl1675,338,052 - 75,340,360 (-)Ensembl
RefSeq Acc Id: NM_173329   ⟹   NP_775451
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21670,342,530 - 70,344,836 (-)NCBI
Rnor_6.01675,338,051 - 75,340,357 (-)NCBI
Rnor_5.01674,952,566 - 74,954,917 (-)NCBI
RGSC_v3.41675,024,375 - 75,026,675 (-)RGD
Celera1668,215,238 - 68,217,544 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_775451 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA91973 (Get FASTA)   NCBI Sequence Viewer  
  AAA91974 (Get FASTA)   NCBI Sequence Viewer  
  EDM08976 (Get FASTA)   NCBI Sequence Viewer  
  Q62715 (Get FASTA)   NCBI Sequence Viewer  
  Q62716 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_775451   ⟸   NM_173329
- Peptide Label: precursor
- UniProtKB: Q62715 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018501   ⟸   ENSRNOT00000018501

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q62715-F1-model_v2 AlphaFold Q62715 1-94 view protein structure
AF-Q62716-F1-model_v2 AlphaFold Q62716 1-94 view protein structure

Transcriptome

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

Promoters
RGD ID:13700202
Promoter ID:EPDNEW_R10726
Type:single initiation site
Name:Defa5_1
Description:defensin alpha 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_6.01675,340,375 - 75,340,435EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727951 AgrOrtholog
BioCyc Gene G2FUF-10838 BioCyc
Ensembl Genes ENSRNOG00000030093 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000018501 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018501 ENTREZGENE, 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:286995 UniProtKB/Swiss-Prot
NCBI Gene 286995 ENTREZGENE
PANTHER PTHR11876 UniProtKB/Swiss-Prot
Pfam Defensin_1 UniProtKB/Swiss-Prot
  Defensin_propep UniProtKB/Swiss-Prot
PhenoGen Defa5 PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot
PROSITE DEFENSIN UniProtKB/Swiss-Prot
SMART DEFSN UniProtKB/Swiss-Prot
UniProt DEF1_RAT UniProtKB/Swiss-Prot
  DEF2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q62716 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-11-25 Defa5  defensin alpha 5  Defa5  defensin, alpha 5, Paneth cell-specific  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-01 Defa5  defensin, alpha 5, Paneth cell-specific  Defa  defensin, alpha 5, Paneth cell-specific  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-09-10 Defa  defensin, alpha 5, Paneth cell-specific  LOC286995  defensin NP-2 precursor  Symbol and Name updated 1299863 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_protein synthesized as precursor proteins, then processed to smaller polypeptide forms 1299571