Defb13 (defensin beta 13) - Rat Genome Database

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Gene: Defb13 (defensin beta 13) Rattus norvegicus
Analyze
Symbol: Defb13
Name: defensin beta 13
RGD ID: 1559883
Description: Predicted to enable lipid binding activity. Predicted to be involved in defense response to bacterium and innate immune response. Predicted to be located in extracellular region. Orthologous to several human genes including DEFB107B (defensin beta 107B); INTERACTS WITH acrylamide; bisphenol A; nitrofen.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BD-13; beta-defensin 13; defensin, beta 13
RGD Orthologs
Human
Mouse
Dog
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81676,831,868 - 76,833,977 (-)NCBIGRCr8
mRatBN7.21670,129,400 - 70,131,509 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,129,625 - 70,131,473 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,403,326 - 75,405,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,866,193 - 78,868,029 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,115,607 - 74,117,443 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,027,131 - 75,028,977 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,027,131 - 75,028,977 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,651,452 - 74,653,298 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,806,640 - 74,808,486 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,013,133 - 68,014,979 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process

Cellular Component

Molecular Function

References

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


Genomics

Comparative Map Data
Defb13
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81676,831,868 - 76,833,977 (-)NCBIGRCr8
mRatBN7.21670,129,400 - 70,131,509 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,129,625 - 70,131,473 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,403,326 - 75,405,162 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01678,866,193 - 78,868,029 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,115,607 - 74,117,443 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,027,131 - 75,028,977 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,027,131 - 75,028,977 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,651,452 - 74,653,298 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41674,806,640 - 74,808,486 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,013,133 - 68,014,979 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
DEFB107B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3887,495,911 - 7,509,311 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl87,811,720 - 7,815,716 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl87,495,911 - 7,509,311 (+)EnsemblGRCh38hg38GRCh38
GRCh3787,353,433 - 7,366,833 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3687,340,778 - 7,354,243 (+)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map8p23.1NCBI
HuRef86,940,286 - 6,940,525 (+)NCBIHuRef
HuRef86,956,308 - 6,956,491 (-)NCBIHuRef
CHM1_187,260,964 - 7,274,426 (-)NCBICHM1_1
T2T-CHM13v2.087,224,926 - 7,228,864 (+)NCBIT2T-CHM13v2.0
Defb13
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39822,436,771 - 22,438,866 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl822,436,778 - 22,438,866 (+)EnsemblGRCm39 Ensembl
GRCm38821,946,755 - 21,948,622 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl821,946,762 - 21,948,850 (+)EnsemblGRCm38mm10GRCm38
MGSCv37823,057,234 - 23,059,094 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36823,412,336 - 23,414,395 (+)NCBIMGSCv36mm8
Celera823,441,733 - 23,443,619 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map810.68NCBI
CBD107
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11659,041,476 - 59,046,080 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1659,041,501 - 59,045,431 (+)EnsemblCanFam3.1canFam3CanFam3.1
ROS_Cfam_1.01657,002,572 - 57,006,481 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1657,002,680 - 57,006,456 (-)EnsemblROS_Cfam_1.0 Ensembl
UU_Cfam_GSD_1.01655,388,332 - 55,393,497 (-)NCBIUU_Cfam_GSD_1.0

Variants

.
Variants in Defb13
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:25
Interacting mature miRNAs:26
Transcripts:ENSRNOT00000058071
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
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
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 hepatobiliary system renal system reproductive system
High
Medium
Low 21 4
Below cutoff 2 1 1 1 4 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058071   ⟹   ENSRNOP00000054879
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,129,625 - 70,131,473 (-)Ensembl
Rnor_6.0 Ensembl1675,027,131 - 75,028,977 (-)Ensembl
RefSeq Acc Id: NM_001037503   ⟹   NP_001032592
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81676,831,868 - 76,833,977 (-)NCBI
mRatBN7.21670,129,400 - 70,131,509 (-)NCBI
Rnor_6.01675,027,131 - 75,028,977 (-)NCBI
Rnor_5.01674,651,452 - 74,653,298 (-)NCBI
RGSC_v3.41674,806,640 - 74,808,486 (-)RGD
Celera1668,013,133 - 68,014,979 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032592 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51884 (Get FASTA)   NCBI Sequence Viewer  
  EDM08979 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000054879
  ENSRNOP00000054879.1
  ENSRNOP00055011001
  ENSRNOP00060033953
  ENSRNOP00065009797
GenBank Protein Q32ZH8 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001032592   ⟸   NM_001037503
- Peptide Label: precursor
- UniProtKB: Q32ZH8 (UniProtKB/Swiss-Prot),   A6IW93 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000054879   ⟸   ENSRNOT00000058071
Protein Domains
Beta-defensin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZH8-F1-model_v2 AlphaFold Q32ZH8 1-66 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:1559883 AgrOrtholog
BioCyc Gene G2FUF-10848 BioCyc
Ensembl Genes ENSRNOG00000038157 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055008099 UniProtKB/Swiss-Prot
  ENSRNOG00060023706 UniProtKB/Swiss-Prot
  ENSRNOG00065008339 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000058071 ENTREZGENE
  ENSRNOT00000058071.2 UniProtKB/Swiss-Prot
  ENSRNOT00055013699 UniProtKB/Swiss-Prot
  ENSRNOT00060041025 UniProtKB/Swiss-Prot
  ENSRNOT00065013230 UniProtKB/Swiss-Prot
InterPro Beta_defensin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:641626 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 641626 ENTREZGENE
Pfam Defensin_beta_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Defb13 PhenoGen
RatGTEx ENSRNOG00000038157 RatGTEx
  ENSRNOG00055008099 RatGTEx
  ENSRNOG00060023706 RatGTEx
  ENSRNOG00065008339 RatGTEx
UniProt A6IW93 ENTREZGENE, UniProtKB/TrEMBL
  DFB13_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb13  defensin beta 13    defensin, beta 13  Name updated 1299863 APPROVED
2006-02-09 Defb13  defensin, beta 13      Symbol and Name status set to provisional 70820 PROVISIONAL