Defb41 (defensin beta 41) - Rat Genome Database

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Gene: Defb41 (defensin beta 41) Rattus norvegicus
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Symbol: Defb41
Name: defensin beta 41
RGD ID: 1562459
Description: Predicted to enable CCR6 chemokine receptor binding activity and chemoattractant activity. Predicted to be involved in cell chemotaxis and defense response to bacterium. Predicted to be located in cytosol. Predicted to be active in extracellular space. Orthologous to several human genes including DEFB130B (defensin beta 130B).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: beta-defensin 130; beta-defensin 130-like; beta-defensin 41
RGD Orthologs
Human
Mouse
Squirrel
Pig
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81541,430,982 - 41,435,053 (+)NCBIGRCr8
mRatBN7.21537,254,995 - 37,259,066 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1537,255,022 - 37,257,543 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1539,120,104 - 39,122,631 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01540,270,910 - 40,273,437 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01538,715,660 - 38,718,181 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01546,179,787 - 46,182,308 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1546,179,787 - 46,182,308 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01549,945,731 - 49,948,252 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,267,937 - 42,270,458 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1536,940,730 - 36,943,251 (+)NCBICelera
Cytogenetic Map15p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. GOA pipeline RGD automated data pipeline
Additional References at PubMed
PMID:16033865   PMID:28181499  


Genomics

Comparative Map Data
Defb41
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81541,430,982 - 41,435,053 (+)NCBIGRCr8
mRatBN7.21537,254,995 - 37,259,066 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1537,255,022 - 37,257,543 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1539,120,104 - 39,122,631 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01540,270,910 - 40,273,437 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01538,715,660 - 38,718,181 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01546,179,787 - 46,182,308 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1546,179,787 - 46,182,308 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01549,945,731 - 49,948,252 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,267,937 - 42,270,458 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1536,940,730 - 36,943,251 (+)NCBICelera
Cytogenetic Map15p12NCBI
DEFB130B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38812,064,389 - 12,071,747 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl812,064,389 - 12,071,747 (-)EnsemblGRCh38hg38GRCh38
GRCh37811,921,898 - 11,929,256 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36811,959,307 - 11,966,665 (-)NCBINCBI36Build 36hg18NCBI36
Cytogenetic Map8p23.1NCBI
CHM1_1811,987,173 - 11,987,354 (-)NCBICHM1_1
T2T-CHM13v2.087,662,435 - 7,669,789 (+)NCBIT2T-CHM13v2.0
Defb47
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391463,229,824 - 63,238,629 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1463,235,526 - 63,238,609 (+)EnsemblGRCm39 Ensembl
GRCm381462,992,375 - 63,001,180 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1462,998,077 - 63,001,160 (+)EnsemblGRCm38mm10GRCm38
MGSCv371463,616,914 - 63,619,997 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361461,952,212 - 61,955,176 (+)NCBIMGSCv36mm8
Celera1460,757,839 - 60,760,903 (+)NCBICelera
Cytogenetic Map14D1NCBI
cM Map1433.23NCBI
Defb130b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049435,079,816 - 5,121,360 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493711730,234 - 38,633 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC110257049
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11538,189,899 - 38,195,975 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Defb130b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475825,503,327 - 25,506,979 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Defb41
22 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:17
Count of miRNA genes:16
Interacting mature miRNAs:17
Transcripts:ENSRNOT00000059213
Prediction methods:Miranda, Rnahybrid, Targetscan
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
731170Pur3Proteinuria QTL 32.30.0005urine protein amount (VT:0005160)urine protein excretion rate (CMO:0000759)15141686771Rat
1641887Alcrsp14Alcohol response QTL 14response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)15142356671Rat
2298549Neuinf12Neuroinflammation QTL 123.5nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)15155302115Rat
10401805Kidm51Kidney mass QTL 51kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1530632945306329Rat
738017Hcas7Hepatocarcinoma susceptibility QTL 72.91liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)15226636846921453Rat
1582251Gluco24Glucose level QTL 243.20.0008blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)15553075650530756Rat
631273Lecl2Lens clarity QTL 20.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)151059608955596089Rat
2300167Bmd63Bone mineral density QTL 635.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2300173Bmd62Bone mineral density QTL 6212.80.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)151111114256111142Rat
2293688Bss29Bone structure and strength QTL 295.310.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)151111114256111142Rat
2317750Glom26Glomerulus QTL 264.3urine protein amount (VT:0005160)urine protein level (CMO:0000591)151249614165205939Rat
61424Scl1Serum cholesterol level QTL 17.70.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)151672552880672115Rat
1331729Rf42Renal function QTL 423.071kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)151736289773690657Rat
2324620Coatc3Coat color QTL 3coat/hair pigmentation trait (VT:0010463)pigmented coat/hair area to total coat/hair area ratio (CMO:0001810)151985656646187442Rat
10054130Srcrt8Stress Responsive Cort QTL 82.180.0085blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)152211793367117933Rat
1578646Bmd18Bone mineral density QTL 185.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)152280624098288169Rat
1578647Bmd17Bone mineral density QTL 174femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)152280624098288169Rat
1578660Bss19Bone structure and strength QTL 194.3femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)152280624098288169Rat
1582214Stl21Serum triglyceride level QTL 213.10.022blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)152803066582262678Rat
1582227Gluco30Glucose level QTL 303.60.0003blood glucose amount (VT:0000188)absolute change in blood glucose level area under curve (CMO:0002034)152803066582262678Rat
1582228Epfw3Epididymal fat weight QTL 34.10.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
1582242Gluco28Glucose level QTL 283.30.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)152803066582262678Rat
1582244Bw79Body weight QTL 7940.0002epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)152803066582262678Rat
2293691Bmd37Bone mineral density QTL 376.60.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)153361105871477291Rat
2293686Bmd36Bone mineral density QTL 367.40.0001femur strength trait (VT:0010010)femoral neck ultimate force (CMO:0001703)153361105871477291Rat
1598828Glom14Glomerulus QTL 142.5kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)153405413979054139Rat

Markers in Region
AU049503  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21537,253,927 - 37,254,157 (+)MAPPERmRatBN7.2
Rnor_6.01546,178,695 - 46,178,922NCBIRnor6.0
Rnor_5.01549,944,639 - 49,944,866UniSTSRnor5.0
RGSC_v3.41542,266,845 - 42,267,072UniSTSRGSC3.4
Celera1536,939,638 - 36,939,865UniSTS
Cytogenetic Map15p12UniSTS


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

hemolymphoid system nervous system renal system reproductive system
High
Medium
Low 1 1 6
Below cutoff 1 2 6 7

Sequence


RefSeq Acc Id: ENSRNOT00000059213   ⟹   ENSRNOP00000055983
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1537,255,022 - 37,257,543 (+)Ensembl
Rnor_6.0 Ensembl1546,179,787 - 46,182,308 (+)Ensembl
RefSeq Acc Id: NM_001037526   ⟹   NP_001032615
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81541,430,982 - 41,435,053 (+)NCBI
mRatBN7.21537,254,995 - 37,259,066 (+)NCBI
Rnor_6.01546,179,787 - 46,182,308 (+)NCBI
Rnor_5.01549,945,731 - 49,948,252 (+)NCBI
RGSC_v3.41542,267,937 - 42,270,458 (+)RGD
Celera1536,940,730 - 36,943,251 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032615 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51907 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000055983
  ENSRNOP00000055983.1
RefSeq Acc Id: NP_001032615   ⟸   NM_001037526
- Peptide Label: precursor
- UniProtKB: Q32ZF5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000055983   ⟸   ENSRNOT00000059213

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZF5-F1-model_v2 AlphaFold Q32ZF5 1-79 view protein structure

Transcriptome

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

Promoters
RGD ID:13699772
Promoter ID:EPDNEW_R10295
Type:single initiation site
Name:Defb41_1
Description:defensin beta 41
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_6.01546,179,760 - 46,179,820EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562459 AgrOrtholog
BioCyc Gene G2FUF-13442 BioCyc
Ensembl Genes ENSRNOG00000038760 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000059213 ENTREZGENE
  ENSRNOT00000059213.2 UniProtKB/TrEMBL
InterPro Defensin_beta UniProtKB/TrEMBL
KEGG Report rno:641650 UniProtKB/TrEMBL
NCBI Gene 641650 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/TrEMBL
  BETA-DEFENSIN 130A-RELATED UniProtKB/TrEMBL
Pfam Defensin_beta UniProtKB/TrEMBL
PhenoGen Defb41 PhenoGen
RatGTEx ENSRNOG00000038760 RatGTEx
Superfamily-SCOP Defensin-like UniProtKB/TrEMBL
UniProt Q32ZF5 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb41  defensin beta 41    beta-defensin 41  Name updated 1299863 APPROVED
2006-02-09 Defb41  beta-defensin 41      Symbol and Name status set to provisional 70820 PROVISIONAL