Defb40 (defensin beta 40) - Rat Genome Database

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Gene: Defb40 (defensin beta 40) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defb40
Name: defensin beta 40
RGD ID: 1563712
Description: Predicted to enable CCR6 chemokine receptor binding activity. Predicted to be involved in defense response to Gram-negative bacterium; defense response to Gram-positive bacterium; and innate immune response in mucosa. Predicted to be located in extracellular region. Predicted to be active in extracellular space; INTERACTS WITH 1,2-dimethylhydrazine; bisphenol A; cadmium dichloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-defensin 40
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,526,834 - 77,529,918 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,526,834 - 77,529,918 (+)EnsemblGRCr8
mRatBN7.21670,824,419 - 70,827,502 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,824,522 - 70,827,449 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1676,101,389 - 76,104,317 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,556,598 - 79,559,529 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,806,012 - 74,808,945 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,702,347 - 75,705,489 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,702,347 - 75,705,489 (+)Ensemblrn6Rnor6.0
Rnor_5.01675,302,719 - 75,305,861 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,606,142 - 75,609,070 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,676,337 - 68,679,265 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse:




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

Biological Process

Cellular Component

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:16033865  


Genomics

Variants

.
Variants in Defb40
35 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:58
Count of miRNA genes:55
Interacting mature miRNAs:56
Transcripts:ENSRNOT00000048827
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 (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


Expression

RNA-SEQ Expression

ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
2 1 1 2 10 2 1 2 8 2 1

Sequence


Ensembl Acc Id: ENSRNOT00000048827   ⟹   ENSRNOP00000049483
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,526,834 - 77,529,918 (+)Ensembl
mRatBN7.2 Ensembl1670,824,522 - 70,827,449 (+)Ensembl
Rnor_6.0 Ensembl1675,702,347 - 75,705,489 (+)Ensembl
RefSeq Acc Id: NM_001037511   ⟹   NP_001032600
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,526,834 - 77,529,918 (+)NCBI
mRatBN7.21670,824,419 - 70,827,502 (+)NCBI
Rnor_6.01675,702,347 - 75,705,489 (+)NCBI
Rnor_5.01675,302,719 - 75,305,861 (+)NCBI
RGSC_v3.41675,606,142 - 75,609,070 (+)RGD
Celera1668,676,337 - 68,679,265 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032600 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51906 (Get FASTA)   NCBI Sequence Viewer  
  EDM08962 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000049483
  ENSRNOP00000049483.1
RefSeq Acc Id: NP_001032600   ⟸   NM_001037511
- Peptide Label: precursor
- UniProtKB: Q32ZF6 (UniProtKB/TrEMBL),   A6IWB0 (UniProtKB/TrEMBL),   F7F734 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000049483   ⟸   ENSRNOT00000048827
Protein Domains
Beta-defensin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZF6-F1-model_v2 AlphaFold Q32ZF6 1-73 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1563712 AgrOrtholog
BioCyc Gene G2FUF-10810 BioCyc
Ensembl Genes ENSRNOG00000033538 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000048827 ENTREZGENE
  ENSRNOT00000048827.3 UniProtKB/TrEMBL
InterPro Defensin_beta UniProtKB/TrEMBL
KEGG Report rno:641637 UniProtKB/TrEMBL
NCBI Gene 641637 ENTREZGENE
PANTHER BETA-DEFENSIN 40 UniProtKB/TrEMBL
  BETA-DEFENSIN-RELATED UniProtKB/TrEMBL
Pfam Defensin_beta UniProtKB/TrEMBL
PhenoGen Defb40 PhenoGen
PROSITE PROKAR_LIPOPROTEIN UniProtKB/TrEMBL
RatGTEx ENSRNOG00000033538 RatGTEx
Superfamily-SCOP Defensin-like UniProtKB/TrEMBL
UniProt A6IWB0 ENTREZGENE, UniProtKB/TrEMBL
  F7F734 ENTREZGENE, UniProtKB/TrEMBL
  Q32ZF6 ENTREZGENE
UniProt Secondary Q32ZF6 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb40  defensin beta 40    beta-defensin 40  Name updated 1299863 APPROVED
2006-02-09 Defb40  beta-defensin 40      Symbol and Name status set to provisional 70820 PROVISIONAL