Defa6 (defensin alpha 6) - Rat Genome Database

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Gene: Defa6 (defensin alpha 6) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defa6
Name: defensin alpha 6
RGD ID: 1562293
Description: Predicted to be involved in cellular response to lipopolysaccharide; defense response to other organism; and disruption of plasma membrane integrity in another organism. Predicted to be active in extracellular space. Orthologous to several human genes including DEFA1 (defensin alpha 1); DEFA1B (defensin alpha 1B); and DEFA3 (defensin alpha 3).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-defensin 6
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,107,681 - 77,108,695 (+)NCBIGRCr8
mRatBN7.21670,405,223 - 70,406,237 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,405,268 - 70,406,142 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,678,977 - 75,679,851 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,132,348 - 79,133,222 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,381,776 - 74,382,650 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,400,781 - 75,401,655 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,400,781 - 75,401,655 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01675,017,486 - 75,018,360 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,087,445 - 75,088,319 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1668,277,794 - 68,278,668 (+)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:7927786   PMID:11248802  


Genomics

Variants

.
Variants in Defa6
17 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:114
Count of miRNA genes:103
Interacting mature miRNAs:105
Transcripts:ENSRNOT00000050112
Prediction methods:Microtar, 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
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
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
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
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

alimentary part of gastrointestinal system
appendage
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
mesenchyme
mesoderm
reproductive system
respiratory system
4 1 6 6 1 5 1 11 6 8 5

Sequence


Ensembl Acc Id: ENSRNOT00000050112   ⟹   ENSRNOP00000046539
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1670,405,268 - 70,406,142 (+)Ensembl
Rnor_6.0 Ensembl1675,400,781 - 75,401,655 (+)Ensembl
RefSeq Acc Id: NM_001033076   ⟹   NP_001028248
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,107,681 - 77,108,695 (+)NCBI
mRatBN7.21670,405,223 - 70,406,237 (+)NCBI
Rnor_6.01675,400,781 - 75,401,655 (+)NCBI
Rnor_5.01675,017,486 - 75,018,360 (+)NCBI
RGSC_v3.41675,087,445 - 75,088,319 (+)RGD
Celera1668,277,794 - 68,278,668 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001028248 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAT68749 (Get FASTA)   NCBI Sequence Viewer  
  AAT68757 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000046539.1
RefSeq Acc Id: NP_001028248   ⟸   NM_001033076
- Peptide Label: precursor
- UniProtKB: Q4JEI8 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000046539   ⟸   ENSRNOT00000050112
Protein Domains
Alpha-defensin N-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q4JEI8-F1-model_v2 AlphaFold Q4JEI8 1-95 view protein structure

Transcriptome

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

Promoters
RGD ID:13700205
Promoter ID:EPDNEW_R10729
Type:single initiation site
Name:Defa6_1
Description:defensin alpha 6
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_6.01675,400,738 - 75,400,798EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562293 AgrOrtholog
BioCyc Gene G2FUF-10833 BioCyc
Ensembl Genes ENSRNOG00000029522 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000050112.2 UniProtKB/TrEMBL
InterPro Alpha-defensin UniProtKB/TrEMBL
  Defensin_propep UniProtKB/TrEMBL
  Defensin_RK-1 UniProtKB/TrEMBL
KEGG Report rno:613223 UniProtKB/TrEMBL
NCBI Gene 613223 ENTREZGENE
PANTHER ALPHA-DEFENSIN 1-RELATED UniProtKB/TrEMBL
  PTHR11876 UniProtKB/TrEMBL
Pfam Defensin_propep UniProtKB/TrEMBL
  Defensin_RK-1 UniProtKB/TrEMBL
PhenoGen Defa6 PhenoGen
PIRSF Alpha-defensin UniProtKB/TrEMBL
RatGTEx ENSRNOG00000029522 RatGTEx
SMART Defensin_propep UniProtKB/TrEMBL
UniProt Q4JEI8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2006-02-09 Defa6  defensin alpha 6      Symbol and Name status set to provisional 70820 PROVISIONAL