Defb30 (defensin beta 30) - Rat Genome Database

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Gene: Defb30 (defensin beta 30) Rattus norvegicus
Analyze
Symbol: Defb30
Name: defensin beta 30
RGD ID: 1559641
Description: Predicted to be involved in defense response to bacterium and innate immune response. Predicted to be located in extracellular region. Orthologous to human DEFB135 (defensin beta 135); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BD-30; beta-defensin 30; defensin, beta 30
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21537,296,636 - 37,298,429 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1537,296,602 - 37,298,479 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1539,161,730 - 39,163,521 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01540,312,540 - 40,314,331 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01538,757,272 - 38,759,065 (-)NCBIRnor_WKY
Rnor_6.01546,220,136 - 46,223,429 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1546,221,592 - 46,223,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01549,987,536 - 49,989,329 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,310,906 - 42,312,699 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1536,982,808 - 36,984,601 (-)NCBICelera
Cytogenetic Map15p12NCBI
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

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   PMID:16457734  


Genomics

Comparative Map Data
Defb30
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21537,296,636 - 37,298,429 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1537,296,602 - 37,298,479 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1539,161,730 - 39,163,521 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01540,312,540 - 40,314,331 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01538,757,272 - 38,759,065 (-)NCBIRnor_WKY
Rnor_6.01546,220,136 - 46,223,429 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1546,221,592 - 46,223,385 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01549,987,536 - 49,989,329 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41542,310,906 - 42,312,699 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1536,982,808 - 36,984,601 (-)NCBICelera
Cytogenetic Map15p12NCBI
DEFB135
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38811,982,256 - 11,984,590 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl811,982,256 - 11,984,590 (+)EnsemblGRCh38hg38GRCh38
GRCh37811,839,765 - 11,842,099 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36811,877,239 - 11,879,508 (+)NCBINCBI36Build 36hg18NCBI36
Celera810,969,157 - 10,971,459 (+)NCBICelera
Cytogenetic Map8p23.1NCBI
HuRef810,770,570 - 10,772,839 (+)NCBIHuRef
CHM1_1812,281,236 - 12,283,505 (+)NCBICHM1_1
T2T-CHM13v2.087,755,679 - 7,758,013 (-)NCBIT2T-CHM13v2.0
Defb30
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391463,271,536 - 63,275,295 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1463,271,536 - 63,287,409 (-)EnsemblGRCm39 Ensembl
GRCm381463,034,087 - 63,037,846 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1463,034,087 - 63,049,960 (-)EnsemblGRCm38mm10GRCm38
MGSCv371463,652,924 - 63,656,683 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361461,988,197 - 61,991,943 (-)NCBIMGSCv36mm8
Celera1460,794,679 - 60,798,445 (-)NCBICelera
Cytogenetic Map14D1NCBI
Defb135
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495540353,199,675 - 53,211,089 (+)NCBIChiLan1.0ChiLan1.0
DEFB135
(Pan paniscus - bonobo/pygmy chimpanzee)
No map positions available.
DEFB135
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12525,926,517 - 25,927,860 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2525,926,568 - 25,927,854 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2526,583,582 - 26,584,925 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02526,081,472 - 26,082,815 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2526,081,561 - 26,082,727 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12526,026,253 - 26,027,595 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02525,930,920 - 25,932,262 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02526,082,150 - 26,083,492 (-)NCBIUU_Cfam_GSD_1.0
DEFB135
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11415,143,118 - 15,145,096 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21416,308,942 - 16,333,926 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DEFB135
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl87,154,358 - 7,156,627 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605235,280,853 - 35,283,132 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Defb30
13 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:87
Count of miRNA genes:73
Interacting mature miRNAs:76
Transcripts:ENSRNOT00000059211
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
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


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 nervous system reproductive system
High
Medium
Low 4 4
Below cutoff 4 2 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000059211   ⟹   ENSRNOP00000055981
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1537,296,602 - 37,298,479 (-)Ensembl
Rnor_6.0 Ensembl1546,221,592 - 46,223,385 (-)Ensembl
RefSeq Acc Id: NM_001037531   ⟹   NP_001032620
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21537,296,636 - 37,298,429 (-)NCBI
Rnor_6.01546,221,592 - 46,223,385 (-)NCBI
Rnor_5.01549,987,536 - 49,989,329 (-)NCBI
RGSC_v3.41542,310,906 - 42,312,699 (-)RGD
Celera1536,982,808 - 36,984,601 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032620 (Get FASTA)   NCBI Sequence Viewer  
  NP_001399513 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT51900 (Get FASTA)   NCBI Sequence Viewer  
  AAU04550 (Get FASTA)   NCBI Sequence Viewer  
  Q32ZG2 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032620   ⟸   NM_001037531
- Peptide Label: precursor
- UniProtKB: Q32ZG2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000055981   ⟸   ENSRNOT00000059211

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q32ZG2-F1-model_v2 AlphaFold Q32ZG2 1-75 view protein structure

Transcriptome

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

Promoters
RGD ID:13699774
Promoter ID:EPDNEW_R10296
Type:single initiation site
Name:Defb30_1
Description:defensin beta 30
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_6.01546,223,424 - 46,223,484EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1559641 AgrOrtholog
BioCyc Gene G2FUF-13440 BioCyc
Ensembl Genes ENSRNOG00000038758 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000055981 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000059211 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro Beta_defensin UniProtKB/Swiss-Prot
KEGG Report rno:641656 UniProtKB/Swiss-Prot
NCBI Gene 641656 ENTREZGENE
Pfam Defensin_beta_2 UniProtKB/Swiss-Prot
PhenoGen Defb30 PhenoGen
UniProt DFB30_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-11-07 Defb30  defensin beta 30    beta-defensin 30  Name updated 1299863 APPROVED
2006-02-09 Defb30  beta-defensin 30      Symbol and Name status set to provisional 70820 PROVISIONAL