Defb20 (defensin beta 20) - Rat Genome Database

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Gene: Defb20 (defensin beta 20) Rattus norvegicus
Analyze
Symbol: Defb20
Name: defensin beta 20
RGD ID: 1565177
Description: Predicted to be involved in defense response to Gram-negative bacterium and defense response to Gram-positive bacterium. Predicted to be located in extracellular region. Orthologous to human DEFB128 (defensin beta 128); INTERACTS WITH atrazine; Cuprizon; benzo[a]pyrene (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BD-20; beta-defensin 20; defensin, beta 20
RGD Orthologs
Human
Mouse
Chinchilla
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83161,408,395 - 161,411,194 (+)NCBIGRCr8
mRatBN7.23140,948,108 - 140,950,907 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,948,154 - 140,950,777 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3144,853,379 - 144,856,066 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03153,437,228 - 153,439,915 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03151,177,235 - 151,179,900 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03147,952,879 - 147,955,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,952,879 - 147,955,502 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03154,300,300 - 154,301,592 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,804,804 - 142,807,427 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3139,699,738 - 139,702,361 (+)NCBICelera
Cytogenetic Map3q41NCBI
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
atrazine  (EXP)
benzo[a]pyrene  (ISO)
Cuprizon  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

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:15625724   PMID:16033865  


Genomics

Comparative Map Data
Defb20
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83161,408,395 - 161,411,194 (+)NCBIGRCr8
mRatBN7.23140,948,108 - 140,950,907 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,948,154 - 140,950,777 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3144,853,379 - 144,856,066 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03153,437,228 - 153,439,915 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03151,177,235 - 151,179,900 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03147,952,879 - 147,955,502 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,952,879 - 147,955,502 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03154,300,300 - 154,301,592 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,804,804 - 142,807,427 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3139,699,738 - 139,702,361 (+)NCBICelera
Cytogenetic Map3q41NCBI
DEFB128
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3820187,853 - 189,711 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl20187,853 - 189,711 (-)EnsemblGRCh38hg38GRCh38
GRCh3720168,494 - 170,352 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 3620116,527 - 118,264 (-)NCBINCBI36Build 36hg18NCBI36
Celera20263,359 - 265,096 (-)NCBICelera
Cytogenetic Map20p13NCBI
HuRef20119,417 - 121,154 (-)NCBIHuRef
CHM1_120168,560 - 170,297 (-)NCBICHM1_1
T2T-CHM13v2.020230,387 - 232,245 (-)NCBIT2T-CHM13v2.0
Defb20
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392152,318,983 - 152,321,645 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2152,318,983 - 152,321,854 (+)EnsemblGRCm39 Ensembl
GRCm382152,477,063 - 152,479,934 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2152,477,063 - 152,479,934 (+)EnsemblGRCm38mm10GRCm38
MGSCv372152,302,799 - 152,305,670 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362152,168,504 - 152,171,375 (+)NCBIMGSCv36mm8
Celera2158,292,563 - 158,295,420 (+)NCBICelera
Cytogenetic Map2H1NCBI
cM Map275.11NCBI
Defb128
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495559764,950 - 66,692 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495559764,950 - 66,692 (-)NCBIChiLan1.0ChiLan1.0
DEFB128
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12420,652,638 - 20,654,574 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2420,652,527 - 20,671,741 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2420,305,580 - 20,307,516 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02421,346,427 - 21,348,363 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2421,346,316 - 21,365,340 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12420,622,473 - 20,624,408 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02420,727,664 - 20,729,599 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02421,158,418 - 21,160,354 (+)NCBIUU_Cfam_GSD_1.0
Defb128
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640169,807,078 - 169,809,261 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493648518,238,442 - 18,240,625 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DEFB128
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1734,963,374 - 34,966,317 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11734,948,185 - 34,965,455 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21739,738,270 - 39,740,120 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DEFB128
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl235,309,523 - 35,311,258 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660787,479,022 - 7,481,034 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Defb128
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247411,249,893 - 1,251,715 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Defb20
26 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:78
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000031922
Prediction methods:Microtar, 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
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)359242096157323038Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3118839124163839124Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
8552952Pigfal13Plasma insulin-like growth factor 1 level QTL 13blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)3138799500169034231Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat


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

nervous system renal system reproductive system
High
Medium
Low 7
Below cutoff 1 1 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000031922   ⟹   ENSRNOP00000031012
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3140,948,154 - 140,950,777 (+)Ensembl
Rnor_6.0 Ensembl3147,952,879 - 147,955,502 (+)Ensembl
RefSeq Acc Id: NM_001037517   ⟹   NP_001032606
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83161,408,395 - 161,411,194 (+)NCBI
mRatBN7.23140,948,108 - 140,950,907 (+)NCBI
Rnor_6.03147,952,879 - 147,955,502 (+)NCBI
Rnor_5.03154,300,300 - 154,301,592 (+)NCBI
RGSC_v3.43142,804,804 - 142,807,427 (+)RGD
Celera3139,699,738 - 139,702,361 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032606 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51890 (Get FASTA)   NCBI Sequence Viewer  
  EDL86067 (Get FASTA)   NCBI Sequence Viewer  
  EDL86068 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000031012
  ENSRNOP00000031012.4
  ENSRNOP00055001682
  ENSRNOP00055035727
  ENSRNOP00060041586
  ENSRNOP00065031670
GenBank Protein Q32ZH2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001032606   ⟸   NM_001037517
- Peptide Label: precursor
- UniProtKB: Q32ZH2 (UniProtKB/Swiss-Prot),   A6KHN8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000031012   ⟸   ENSRNOT00000031922
Protein Domains
Beta-defensin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZH2-F1-model_v2 AlphaFold Q32ZH2 1-96 view protein structure

Transcriptome

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

Promoters
RGD ID:13692540
Promoter ID:EPDNEW_R3065
Type:single initiation site
Name:Defb20_1
Description:defensin beta 20
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_6.03147,952,823 - 147,952,883EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565177 AgrOrtholog
BioCyc Gene G2FUF-47268 BioCyc
Ensembl Genes ENSRNOG00000023384 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOG00055001319 UniProtKB/Swiss-Prot
  ENSRNOG00055025374 UniProtKB/Swiss-Prot
  ENSRNOG00060028694 UniProtKB/Swiss-Prot
  ENSRNOG00065022847 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000031922 ENTREZGENE
  ENSRNOT00000031922.5 UniProtKB/Swiss-Prot
  ENSRNOT00055002162 UniProtKB/Swiss-Prot
  ENSRNOT00055043740 UniProtKB/Swiss-Prot
  ENSRNOT00060049876 UniProtKB/Swiss-Prot
  ENSRNOT00065039014 UniProtKB/Swiss-Prot
InterPro Beta_defensin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:641641 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
NCBI Gene 641641 ENTREZGENE
PANTHER BETA-DEFENSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  BETA-DEFENSIN 123-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Defensin_beta_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Defb20 PhenoGen
RatGTEx ENSRNOG00000023384 RatGTEx
  ENSRNOG00055001319 RatGTEx
  ENSRNOG00055025374 RatGTEx
  ENSRNOG00060028694 RatGTEx
  ENSRNOG00065022847 RatGTEx
UniProt A6KHN7_RAT UniProtKB/TrEMBL
  A6KHN8 ENTREZGENE, UniProtKB/TrEMBL
  DFB20_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb20  defensin beta 20    beta-defensin 20  Name updated 1299863 APPROVED
2006-02-09 Defb20  beta-defensin 20      Symbol and Name status set to provisional 70820 PROVISIONAL