Defb52 (defensin beta 52) - Rat Genome Database

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Gene: Defb52 (defensin beta 52) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defb52
Name: defensin beta 52
RGD ID: 1565394
Description: INTERACTS WITH atrazine; cadmium dichloride; N-methyl-4-phenylpyridinium
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: beta-defensin 52
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,290,591 - 77,293,067 (+)NCBIGRCr8
mRatBN7.21670,588,150 - 70,590,626 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,588,116 - 70,590,626 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,864,979 - 75,867,455 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,310,646 - 79,313,118 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,560,084 - 74,562,556 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,572,014 - 75,574,546 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,572,070 - 75,574,546 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,173,180 - 75,175,695 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,378,657 - 75,381,133 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,449,959 - 68,452,435 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16033865  


Genomics

Variants

.
Variants in Defb52
40 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:32
Count of miRNA genes:31
Interacting mature miRNAs:31
Transcripts:ENSRNOT00000043486
Prediction methods:Microtar, 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
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
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
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
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

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
6 4 6 15 27 32 9 25 9 1 62 36 9 7 25 23

Sequence


Ensembl Acc Id: ENSRNOT00000043486   ⟹   ENSRNOP00000047337
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,588,116 - 70,590,626 (+)Ensembl
Rnor_6.0 Ensembl1675,572,070 - 75,574,546 (+)Ensembl
RefSeq Acc Id: NM_001037524   ⟹   NP_001032613
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,290,591 - 77,293,067 (+)NCBI
mRatBN7.21670,588,150 - 70,590,626 (+)NCBI
Rnor_6.01675,572,070 - 75,574,546 (+)NCBI
Rnor_5.01675,173,180 - 75,175,695 (+)NCBI
RGSC_v3.41675,378,657 - 75,381,133 (+)RGD
Celera1668,449,959 - 68,452,435 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032613 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAY59819 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000047337.3
RefSeq Acc Id: NP_001032613   ⟸   NM_001037524
- Peptide Label: precursor
- UniProtKB: Q30KJ1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000047337   ⟸   ENSRNOT00000043486

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q30KJ1-F1-model_v2 AlphaFold Q30KJ1 1-86 view protein structure

Transcriptome

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

Promoters
RGD ID:13700210
Promoter ID:EPDNEW_R10734
Type:single initiation site
Name:Defb52_1
Description:defensin beta 52
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_6.01675,572,056 - 75,572,116EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565394 AgrOrtholog
BioCyc Gene G2FUF-10823 BioCyc
Ensembl Genes ENSRNOG00000038129 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000043486.3 UniProtKB/TrEMBL
KEGG Report rno:498660 UniProtKB/TrEMBL
NCBI Gene 498660 ENTREZGENE
PhenoGen Defb52 PhenoGen
RatGTEx ENSRNOG00000038129 RatGTEx
UniProt F7FIF5_RAT UniProtKB/TrEMBL
  Q30KJ1 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb52  defensin beta 52    beta-defensin 52  Name updated 1299863 APPROVED
2006-02-09 Defb52  beta-defensin 52      Symbol and Name status set to provisional 70820 PROVISIONAL