Defb28 (defensin beta 28) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Defb28 (defensin beta 28) Rattus norvegicus
Analyze
Symbol: Defb28
Name: defensin beta 28
RGD ID: 1565792
Description: Predicted to be involved in defense response to bacterium and innate immune response. Predicted to be located in extracellular region. Orthologous to human DEFB115 (defensin beta 115); INTERACTS WITH bisphenol A; aflatoxin B1 (ortholog); CGP 52608 (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: beta-defensin 115; beta-defensin 28
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83161,448,316 - 161,454,051 (+)NCBIGRCr8
mRatBN7.23140,988,032 - 140,993,767 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,988,032 - 140,991,015 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03147,992,754 - 147,995,911 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,992,754 - 147,994,616 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03154,337,607 - 154,340,662 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,838,348 - 142,853,944 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3139,738,883 - 139,742,040 (+)NCBICelera
Cytogenetic Map3q41NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:16033865  


Genomics

Comparative Map Data
Defb28
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83161,448,316 - 161,454,051 (+)NCBIGRCr8
mRatBN7.23140,988,032 - 140,993,767 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3140,988,032 - 140,991,015 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.03147,992,754 - 147,995,911 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3147,992,754 - 147,994,616 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03154,337,607 - 154,340,662 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43142,838,348 - 142,853,944 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera3139,738,883 - 139,742,040 (+)NCBICelera
Cytogenetic Map3q41NCBI
DEFB115
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382031,257,664 - 31,259,632 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2031,257,664 - 31,259,632 (+)EnsemblGRCh38hg38GRCh38
GRCh372029,845,467 - 29,847,435 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362029,309,128 - 29,311,096 (+)NCBINCBI36Build 36hg18NCBI36
Celera2026,601,734 - 26,603,702 (+)NCBICelera
Cytogenetic Map20q11.21NCBI
HuRef2026,634,234 - 26,636,202 (+)NCBIHuRef
CHM1_12029,749,417 - 29,751,385 (+)NCBICHM1_1
T2T-CHM13v2.02032,981,800 - 32,983,768 (+)NCBIT2T-CHM13v2.0
Defb28
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392152,360,175 - 152,363,367 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2152,360,175 - 152,363,367 (+)EnsemblGRCm39 Ensembl
GRCm382152,518,255 - 152,521,447 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2152,518,255 - 152,521,447 (+)EnsemblGRCm38mm10GRCm38
MGSCv372152,343,991 - 152,347,183 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362152,209,696 - 152,212,888 (+)NCBIMGSCv36mm8
Celera2158,333,666 - 158,336,858 (+)NCBICelera
Cytogenetic Map2H1NCBI
cM Map275.2NCBI
Defb115
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495542229,676,981 - 29,681,067 (+)NCBIChiLan1.0ChiLan1.0
DEFB115
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22136,951,250 - 36,953,221 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12036,944,347 - 36,946,318 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02027,549,214 - 27,551,185 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12028,185,796 - 28,187,767 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2028,185,796 - 28,187,767 (+)Ensemblpanpan1.1panPan2
Defb115
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640169,896,285 - 169,900,610 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493648518,327,656 - 18,347,183 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DEFB115
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1735,028,972 - 35,031,088 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11735,029,031 - 35,034,148 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21739,835,623 - 39,840,655 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DEFB115
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl235,689,783 - 35,691,760 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605091,265,351 - 91,267,501 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Defb28
42 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:136
Count of miRNA genes:110
Interacting mature miRNAs:116
Transcripts:ENSRNOT00000055412
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
2312673Scl63Serum cholesterol level QTL 630.001blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)398535255168026850Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3130656562169034231Rat
1598877Bp285Blood pressure QTL 2851.50.03arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3120538241165538241Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)398535386161695835Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
2298477Eau4Experimental allergic uveoretinitis QTL 40.0011uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)3137398739169034231Rat
1581568Rf53Renal function QTL 53urine total protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)356395968161299569Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3112681431157681431Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3121056165145956249Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3131635904169034231Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3122438700167438700Rat
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
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
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)397084464142084464Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3127162703168026850Rat
631841Niddm39Non-insulin dependent diabetes mellitus QTL 393.36blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)394856903159898684Rat
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
619618Rf3Renal disease susceptibility QTL 36.50.001urine albumin amount (VT:0002871)urine albumin excretion rate to body weight ratio (CMO:0001270)3107693393152693393Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3121056165157309487Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3140069424146976080Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3130193298161695983Rat
2312659Slep7Serum leptin concentration QTL 70.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)398535255168026850Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)378196190146592722Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3130656562169034231Rat
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
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3124122556169034231Rat
2312670Bw94Body weight QTL 940.01inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)398535255168026850Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)397551417147415807Rat

Markers in Region
D3Got105  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23140,986,979 - 140,987,215 (+)MAPPERmRatBN7.2
Rnor_6.03147,991,702 - 147,991,937NCBIRnor6.0
Rnor_5.03154,336,555 - 154,336,790UniSTSRnor5.0
RGSC_v3.43142,843,554 - 142,843,790RGDRGSC3.4
RGSC_v3.43142,843,555 - 142,843,790UniSTSRGSC3.4
RGSC_v3.13142,749,128 - 142,749,363RGD
Celera3139,737,830 - 139,738,065UniSTS
RH 3.4 Map31272.8UniSTS
RH 3.4 Map31272.8RGD
RH 2.0 Map3844.2RGD
Cytogenetic Map3q41UniSTS


Expression

RNA-SEQ Expression

circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
renal system
reproductive system
respiratory system
4 1 4 3 2 1 2 51 6 43 16 1

Sequence


Ensembl Acc Id: ENSRNOT00000055412   ⟹   ENSRNOP00000052279
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3140,988,032 - 140,991,015 (+)Ensembl
Rnor_6.0 Ensembl3147,992,754 - 147,994,616 (+)Ensembl
RefSeq Acc Id: XM_063285210   ⟹   XP_063141280
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83161,448,316 - 161,454,051 (+)NCBI
Protein Sequences
Protein RefSeqs XP_063141280 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51898 (Get FASTA)   NCBI Sequence Viewer  
  EDL86065 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000052279.4
Ensembl Acc Id: ENSRNOP00000052279   ⟸   ENSRNOT00000055412
RefSeq Acc Id: XP_063141280   ⟸   XM_063285210
Protein Domains
Beta-defensin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZG4-F1-model_v2 AlphaFold Q32ZG4 1-86 view protein structure

Transcriptome

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

Promoters
RGD ID:13692560
Promoter ID:EPDNEW_R3066
Type:single initiation site
Name:Defb28_1
Description:defensin beta 28
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_6.03147,992,742 - 147,992,802EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565792 AgrOrtholog
BioCyc Gene G2FUF-47265 BioCyc
Ensembl Genes ENSRNOG00000036900 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000055412.4 UniProtKB/TrEMBL
InterPro Beta-defensin UniProtKB/TrEMBL
  Beta_defensin UniProtKB/TrEMBL
NCBI Gene 641628 ENTREZGENE
PANTHER BETA-DEFENSIN 115 UniProtKB/TrEMBL
  BETA-DEFENSIN 123-RELATED UniProtKB/TrEMBL
Pfam Defensin_beta_2 UniProtKB/TrEMBL
PhenoGen Defb28 PhenoGen
RatGTEx ENSRNOG00000036900 RatGTEx
UniProt A0A8J8YAJ6_RAT UniProtKB/TrEMBL
  Q32ZG4_RAT UniProtKB/TrEMBL
UniProt Secondary F1M795 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb28  defensin beta 28      Name updated 1299863 APPROVED
2006-02-09 Defb28  defensin beta 28      Symbol and Name status set to provisional 70820 PROVISIONAL