Defa24 (defensin alpha 24) - 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 QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap)  (beta) 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) Overgo Probe Designer
Aging & Age-Related Disease Cancer & Neoplastic Disease Cardiovascular Disease COVID-19 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   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) 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 Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Defa24 (defensin alpha 24) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Defa24
Name: defensin alpha 24
RGD ID: 1304852
Description: Predicted to be involved in cellular response to lipopolysaccharide and defense response to other 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, 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 Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21670,349,550 - 70,350,582 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1670,349,567 - 70,350,603 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1675,623,265 - 75,624,295 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01679,076,135 - 79,077,157 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01674,325,565 - 74,326,587 (-)NCBIRnor_WKY
Rnor_6.01675,345,086 - 75,346,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1675,345,086 - 75,346,122 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01674,959,602 - 74,960,638 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41675,031,404 - 75,032,437 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11675,031,668 - 75,032,702 (-)NCBI
Celera1668,222,273 - 68,222,478 (-)NCBICelera
Cytogenetic Map16q12.5NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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

miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor depth of invasion (CMO:0001888)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat
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
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
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
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system endocrine system hemolymphoid system nervous system renal system reproductive system
High 1
Medium 1
Low 1 1 2
Below cutoff 1 5 5 4 2 9

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000018529   ⟹   ENSRNOP00000018529
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
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
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  
  P82106 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001013071   ⟸   NM_001013053
- Peptide Label: precursor
- UniProtKB: Q4JEI9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000018529   ⟸   ENSRNOT00000018529
Protein Domains
DEFENSIN

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, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000018529 ENTREZGENE
  ENSRNOP00000018529.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000018529 ENTREZGENE
  ENSRNOT00000018529.5 UniProtKB/TrEMBL
InterPro Alpha-defensin UniProtKB/Swiss-Prot
  Alpha-defensin UniProtKB/TrEMBL, UniProtKB/Swiss-Prot
  Alpha-defensin_pro UniProtKB/TrEMBL
  Alpha-defensin_propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:290856 UniProtKB/TrEMBL
NCBI Gene 290856 ENTREZGENE
PANTHER PTHR11876 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Defensin_propep UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Defa24 PhenoGen
PIRSF Alpha-defensin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE DEFENSIN UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt DEF5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q4JEI9 ENTREZGENE, UniProtKB/TrEMBL
  Q6B328_RAT 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
2008-03-04 Defcr24  defensin related cryptdin 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