Defa24 (defensin alpha 24) - Rat Genome Database

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Gene: Defa24 (defensin alpha 24) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defa24
Name: defensin alpha 24
RGD ID: 1304852
Description: Predicted to enable pore-forming activity. Predicted to be involved in defense response to bacterium; defense response to symbiont; and disruption of plasma membrane integrity in another organism. Predicted to be located in extracellular region. 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); INTERACTS WITH 3,3',4,4',5-pentachlorobiphenyl; 6-propyl-2-thiouracil; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: alpha-defensin, 24; Defcr24; Defcr4; defensin 5; defensin 6; defensin 7; defensin related cryptdin 24; defensin related cryptdin 4; defensin, alpha, 24; defensin-5; enteric defensin alpha 5; LOC290856; RD-5; Rd5
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81677,052,014 - 77,053,046 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1677,052,014 - 77,053,046 (-)EnsemblGRCr8
mRatBN7.21670,349,550 - 70,350,582 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,349,567 - 70,350,603 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1675,623,265 - 75,624,295 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01679,076,135 - 79,077,157 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01674,325,565 - 74,326,587 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01675,345,086 - 75,346,122 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,345,086 - 75,346,122 (-)Ensemblrn6Rnor6.0
Rnor_5.01674,959,602 - 74,960,638 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41675,031,404 - 75,032,437 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1668,222,273 - 68,222,478 (-)NCBICelera
RGSC_v3.11675,031,668 - 75,032,702 (-)NCBI
Cytogenetic Map16q12.5NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

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. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10456932   PMID:17878170  


Genomics

Variants

.
Variants in Defa24
10 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:82
Count of miRNA genes:72
Interacting mature miRNAs:75
Transcripts:ENSRNOT00000018529
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 (GRCr8)
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)164445512389455123Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165942871491442908Rat
1298529Arunc1Aerobic running capacity QTL 14exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)163439829479398294Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)163692878281928782Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)164199206486992064Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)164445512389455123Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165942871491442908Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165942871491442908Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164909919691442908Rat
1298527Arunc2Aerobic running capacity QTL 22.9exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)167523528581732231Rat
1357403Slep4Serum leptin concentration QTL 43.91blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)163236104377361043Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
ectoderm
endocrine system
endoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
respiratory system
10 10 6 6 6 18 6 10 2 14 6

Sequence


Ensembl Acc Id: ENSRNOT00000018529   ⟹   ENSRNOP00000018529
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1677,052,014 - 77,053,046 (-)Ensembl
mRatBN7.2 Ensembl1670,349,567 - 70,350,603 (-)Ensembl
Rnor_6.0 Ensembl1675,345,086 - 75,346,122 (-)Ensembl
RefSeq Acc Id: NM_001013053   ⟹   NP_001013071
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81677,052,014 - 77,053,046 (-)NCBI
mRatBN7.21670,349,550 - 70,350,582 (-)NCBI
Rnor_6.01675,345,086 - 75,346,122 (-)NCBI
Rnor_5.01674,959,602 - 74,960,638 (-)NCBI
RGSC_v3.41675,031,404 - 75,032,437 (-)RGD
Celera1668,222,273 - 68,222,478 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013071 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD22963 (Get FASTA)   NCBI Sequence Viewer  
  AAT68756 (Get FASTA)   NCBI Sequence Viewer  
  AAT91348 (Get FASTA)   NCBI Sequence Viewer  
  AAT91349 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000018529
GenBank Protein P82106 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001013071   ⟸   NM_001013053
- Peptide Label: precursor
- UniProtKB: Q4JEI9 (UniProtKB/TrEMBL),   Q6B329 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018529   ⟸   ENSRNOT00000018529
Protein Domains
Mammalian defensins

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P82106-F1-model_v2 AlphaFold P82106 1-93 view protein structure
AF-Q4JEI9-F1-model_v2 AlphaFold Q4JEI9 1-93 view protein structure

Transcriptome

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

Promoters
RGD ID:13700203
Promoter ID:EPDNEW_R10727
Type:single initiation site
Name:Defa24_1
Description:defensin alpha 24
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_6.01675,346,121 - 75,346,181EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304852 AgrOrtholog
BioCyc Gene G2FUF-10837 BioCyc
Ensembl Genes ENSRNOG00000030524 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000018529 ENTREZGENE
InterPro Alpha-defensin UniProtKB/Swiss-Prot
  Alpha-defensin_C UniProtKB/Swiss-Prot
  Alpha-defensin_propep UniProtKB/Swiss-Prot
NCBI Gene 290856 ENTREZGENE
PANTHER ALPHA-DEFENSIN 1-RELATED UniProtKB/Swiss-Prot
  PTHR11876 UniProtKB/Swiss-Prot
Pfam Defensin_propep UniProtKB/Swiss-Prot
PhenoGen Defa24 PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot
PROSITE DEFENSIN UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000030524 RatGTEx
SMART Defensin_propep UniProtKB/Swiss-Prot
UniProt DEF5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4JEI9 ENTREZGENE, UniProtKB/TrEMBL
  Q6B328_RAT UniProtKB/TrEMBL
  Q6B329 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-08-01 Defa24  defensin alpha 24  Defa24  defensin, alpha, 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-06-12 Defa24  defensin, alpha, 24  Defcr24  defensin related cryptdin 24  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Defcr24  defensin related cryptdin 24  Defcr4  defensin related cryptdin 4  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Defcr4  defensin related cryptdin 4  Defcr4_predicted  defensin related cryptdin 4 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Defcr4_predicted  defensin related cryptdin 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED