Ddx3 (DEAD-box helicase 3) - 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: Ddx3 (DEAD-box helicase 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Ddx3 (Ensembl: Ddx3y)
Name: DEAD-box helicase 3 (Ensembl:DEAD-box helicase 3, Y-linked)
RGD ID: 1309586
Description: Predicted to enable RNA binding activity and RNA helicase activity. Predicted to be involved in cell differentiation and gamete generation. Predicted to be active in P granule and nucleus. Human ortholog(s) of this gene implicated in colorectal cancer and syndromic X-linked intellectual disability. Orthologous to human DDX3X (DEAD-box helicase 3 X-linked); PARTICIPATES IN Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Ddx3y; Ddx3yl; DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked; DEAD-box helicase 3, Y-linked; DEAD-box helicase 3, Y-linked like; hypothetical protein LOC364073; LOC364073; Putative ATP-dependent RNA helicase Pl10-like; RGD1309586; similar to probable ATP-dependent RNA helicase - mouse; uncharacterized protein LOC364073
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21398,520,538 - 98,523,707 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1398,520,201 - 98,524,176 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13101,038,725 - 101,041,894 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.013102,425,198 - 102,428,367 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01399,624,705 - 99,627,874 (+)NCBIRnor_WKY
Rnor_6.013105,408,179 - 105,411,348 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13105,408,179 - 105,411,348 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013110,058,379 - 110,061,548 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413103,083,158 - 103,086,327 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.113103,214,426 - 103,275,002 (+)NCBI
Celera1398,023,033 - 98,026,202 (+)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleus  (IBA)
P granule  (IBA)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19946888  


Genomics

Variants

.
Variants in Ddx3
4 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:98
Count of miRNA genes:75
Interacting mature miRNAs:92
Transcripts:ENSRNOT00000003378
Prediction methods: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
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131101056920Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131101056920Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)138897350101631289Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1320605871101339738Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1330395351101056920Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1356056920101056920Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1374862117101339893Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat


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 circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 11
Low 22 10 10 10 1 1 10 8 24 1
Below cutoff 1 21 41 31 10 31 3 4 63 14 5 11 3

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000003378   ⟹   ENSRNOP00000003378
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1398,520,201 - 98,524,176 (+)Ensembl
Rnor_6.0 Ensembl13105,408,179 - 105,411,348 (+)Ensembl
RefSeq Acc Id: NM_001108858   ⟹   NP_001102328
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21398,520,538 - 98,523,707 (+)NCBI
Rnor_6.013105,408,179 - 105,411,348 (+)NCBI
Rnor_5.013110,058,379 - 110,061,548 (+)NCBI
RGSC_v3.413103,083,158 - 103,086,327 (+)RGD
Celera1398,023,033 - 98,026,202 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102328 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94936 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001102328   ⟸   NM_001108858
- UniProtKB: D3ZN21 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000003378   ⟸   ENSRNOT00000003378
Protein Domains
DEAD-box RNA helicase Q   Helicase ATP-binding   Helicase C-terminal

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZN21-F1-model_v2 AlphaFold D3ZN21 1-659 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309586 AgrOrtholog
BioCyc Gene G2FUF-16945 BioCyc
Ensembl Genes ENSRNOG00000002501 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000003378 ENTREZGENE
  ENSRNOP00000003378.3 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000003378 ENTREZGENE
  ENSRNOT00000003378.5 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
InterPro DEAD-like_N UniProtKB/TrEMBL
  DNA/RNA_helicase_C UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAD/DEAH_N UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  RNA-helicase_DEAD-box_CS UniProtKB/TrEMBL
  RNA_helicase_DEAD_Q_motif UniProtKB/TrEMBL
KEGG Report rno:364073 UniProtKB/TrEMBL
NCBI Gene 364073 ENTREZGENE
PANTHER ATP-DEPENDENT RNA HELICASE DBP3 UniProtKB/TrEMBL
  ATP-DEPENDENT RNA HELICASE PL10-RELATED UniProtKB/TrEMBL
Pfam DEAD UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
PhenoGen Ddx3 PhenoGen
PROSITE DEAD_ATP_HELICASE UniProtKB/TrEMBL
  HELICASE_ATP_BIND_1 UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/TrEMBL
  Q_MOTIF UniProtKB/TrEMBL
SMART DEXDc UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt D3ZN21 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2023-03-09 Ddx3  DEAD-box helicase 3  Ddx3yl  DEAD-box helicase 3, Y-linked like  Name and Symbol changed 629549 APPROVED
2023-03-09 Ddx3yl  DEAD-box helicase 3, Y-linked like  Ddx3y  DEAD-box helicase 3, Y-linked  Name and Symbol changed 629549 APPROVED
2017-10-30 Ddx3y  DEAD-box helicase 3, Y-linked  Ddx3y  DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-07-10 Ddx3y  DEAD (Asp-Glu-Ala-Asp) box helicase 3, Y-linked  RGD1309586  similar to probable ATP-dependent RNA helicase - mouse  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1309586  similar to probable ATP-dependent RNA helicase - mouse   RGD1309586_predicted  similar to probable ATP-dependent RNA helicase - mouse (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1309586_predicted  similar to probable ATP-dependent RNA helicase - mouse (predicted)  LOC364073_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC364073_predicted  similar to probable ATP-dependent RNA helicase - mouse (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL