Ddx3x (DEAD-box helicase 3, X-linked) - Rat Genome Database

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Gene: Ddx3x (DEAD-box helicase 3, X-linked) Rattus norvegicus
Analyze
Symbol: Ddx3x
Name: DEAD-box helicase 3, X-linked
RGD ID: 1564771
Description: Predicted to have several functions, including eukaryotic initiation factor 4E binding activity; nucleic acid binding activity; and nucleoside-triphosphatase activity. Predicted to be involved in several processes, including regulation of cellular protein metabolic process; regulation of gene expression; and regulation of signal transduction. Predicted to colocalize with cytosolic small ribosomal subunit and eukaryotic translation initiation factor 3 complex. Human ortholog(s) of this gene implicated in syndromic X-linked intellectual disability. Orthologous to several human genes including DDX3X (DEAD-box helicase 3 X-linked); PARTICIPATES IN Retinoic acid-inducible gene (RIG) I-like receptor signaling pathway; INTERACTS WITH 2,4-dibromophenyl 2,4,5-tribromophenyl ether; 2,6-dinitrotoluene; 3H-1,2-dithiole-3-thione.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: ATP-dependent RNA helicase DDX3X; DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked; DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked; DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X9,479,532 - 9,493,455 (-)NCBI
Rnor_6.0 EnsemblX10,400,366 - 10,413,995 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X10,400,363 - 10,414,010 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X11,198,745 - 11,212,383 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,495,072 - 21,508,690 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX10,011,280 - 10,024,898 (-)NCBICelera
Cytogenetic MapXq12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process
cell differentiation  (IBA)
cellular response to arsenic-containing substance  (ISO)
cellular response to osmotic stress  (ISO)
cellular response to virus  (ISO)
chromosome segregation  (ISO)
DNA duplex unwinding  (IEA)
extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
gamete generation  (IBA)
innate immune response  (ISO)
intracellular signal transduction  (ISO)
intrinsic apoptotic signaling pathway  (ISO)
lipid homeostasis  (ISO)
mature ribosome assembly  (ISO)
negative regulation by host of viral genome replication  (ISO)
negative regulation of apoptotic process  (ISO)
negative regulation of cell growth  (ISO)
negative regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
negative regulation of extrinsic apoptotic signaling pathway via death domain receptors  (ISO)
negative regulation of intrinsic apoptotic signaling pathway  (ISO)
negative regulation of NIK/NF-kappaB signaling  (ISO)
negative regulation of protein-containing complex assembly  (ISO)
negative regulation of translation  (ISO)
positive regulation of apoptotic process  (ISO)
positive regulation of canonical Wnt signaling pathway  (ISO)
positive regulation of cell growth  (ISO)
positive regulation of cysteine-type endopeptidase activity involved in apoptotic process  (ISO)
positive regulation of G1/S transition of mitotic cell cycle  (ISO)
positive regulation of gene expression  (ISO)
positive regulation of interferon-alpha production  (ISO)
positive regulation of interferon-beta production  (ISO)
positive regulation of NIK/NF-kappaB signaling  (ISO)
positive regulation of NLRP3 inflammasome complex assembly  (ISO)
positive regulation of protein acetylation  (ISO)
positive regulation of protein autophosphorylation  (ISO)
positive regulation of protein K63-linked ubiquitination  (ISO)
positive regulation of protein serine/threonine kinase activity  (ISO)
positive regulation of toll-like receptor 7 signaling pathway  (ISO)
positive regulation of toll-like receptor 8 signaling pathway  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
positive regulation of transcription, DNA-templated  (ISO)
positive regulation of translation  (ISO)
positive regulation of translation in response to endoplasmic reticulum stress  (ISO)
positive regulation of translational initiation  (ISO)
positive regulation of viral genome replication  (ISO)
primary miRNA processing  (ISO)
protein localization to cytoplasmic stress granule  (ISO)
response to virus  (ISO)
RNA secondary structure unwinding  (ISO)
stress granule assembly  (ISO)
translational initiation  (ISO)
Wnt signaling pathway  (ISO)

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:10074132   PMID:10329544   PMID:16301996   PMID:16818630   PMID:17667941   PMID:18583960   PMID:18596238   PMID:18628297   PMID:18636090   PMID:18846110   PMID:19056867   PMID:19199708  
PMID:20458337   PMID:20837705   PMID:20862261   PMID:21589879   PMID:21700703   PMID:21730191   PMID:21883093   PMID:22082260   PMID:22323517   PMID:22658674   PMID:22681889   PMID:22872150  
PMID:23413191   PMID:24380861   PMID:24625528   PMID:24965446   PMID:25468996   PMID:26100019   PMID:26235985   PMID:27546789   PMID:27736973   PMID:27980081   PMID:28128295   PMID:28733330  
PMID:28819115   PMID:28842590   PMID:29062139   PMID:29899501   PMID:30341167   PMID:31511697  


Genomics

Comparative Map Data
Ddx3x
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X9,479,532 - 9,493,455 (-)NCBI
Rnor_6.0 EnsemblX10,400,366 - 10,413,995 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X10,400,363 - 10,414,010 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X11,198,745 - 11,212,383 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X21,495,072 - 21,508,690 (-)NCBIRGSC3.4rn4RGSC3.4
CeleraX10,011,280 - 10,024,898 (-)NCBICelera
Cytogenetic MapXq12NCBI
DDX3X
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX41,333,284 - 41,364,472 (+)EnsemblGRCh38hg38GRCh38
GRCh38.p13 EnsemblX41,333,348 - 41,364,472 (+)EnsemblGRCh38hg38GRCh38
GRCh38X41,333,308 - 41,364,472 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X41,192,561 - 41,223,725 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X41,077,595 - 41,094,471 (+)NCBINCBI36hg18NCBI36
Build 34X40,948,904 - 40,979,978NCBI
CeleraX45,333,407 - 45,350,283 (+)NCBI
Cytogenetic MapXp11.4NCBI
HuRefX38,924,970 - 38,941,587 (+)NCBIHuRef
CHM1_1X41,225,277 - 41,256,447 (+)NCBICHM1_1
Ddx3x
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X13,147,261 - 13,160,222 (+)NCBIGRCm39mm39
GRCm39 EnsemblX13,147,209 - 13,160,291 (+)Ensembl
GRCm38X13,280,496 - 13,293,988 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX13,280,970 - 13,294,052 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X12,858,148 - 12,871,109 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X12,437,997 - 12,449,573 (+)NCBImm8
CeleraX10,940,806 - 10,968,272 (+)NCBICelera
Cytogenetic MapXA1.1NCBI
cM MapX8.17NCBI
Ddx3x
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555651,386,973 - 1,404,220 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555651,387,043 - 1,403,624 (-)NCBIChiLan1.0ChiLan1.0
DDX3X
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X41,474,515 - 41,491,479 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX41,475,116 - 41,505,837 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X33,780,381 - 33,796,829 (+)NCBIMhudiblu_PPA_v0panPan3
DDX3X
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X35,759,367 - 35,789,759 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX35,759,416 - 35,789,774 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX23,107,814 - 23,138,223 (+)NCBI
ROS_Cfam_1.0X35,809,592 - 35,840,330 (+)NCBI
UMICH_Zoey_3.1X35,887,325 - 35,918,053 (+)NCBI
UNSW_CanFamBas_1.0X35,859,851 - 35,889,927 (+)NCBI
UU_Cfam_GSD_1.0X35,902,946 - 35,933,679 (+)NCBI
Ddx3x
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X27,967,669 - 27,979,844 (+)NCBI
SpeTri2.0NW_0049365027,770,896 - 7,820,555 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX3X
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX36,988,031 - 37,044,769 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X36,988,031 - 37,005,496 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X41,162,232 - 41,177,756 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DDX3X
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X38,513,251 - 38,539,982 (+)NCBI
Ddx3x
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476214,290,267 - 14,305,437 (-)NCBI

Position Markers
L25126  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,481,913 - 9,482,019 (+)MAPPER
Rnor_6.0X10,402,745 - 10,402,850NCBIRnor6.0
Rnor_5.0X11,201,127 - 11,201,232UniSTSRnor5.0
RGSC_v3.4X21,497,451 - 21,497,556UniSTSRGSC3.4
CeleraX10,013,659 - 10,013,764UniSTS
Cytogenetic MapXq12UniSTS
SHGC-33274  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,480,579 - 9,480,704 (+)MAPPER
Rnor_6.0X10,401,411 - 10,401,535NCBIRnor6.0
Rnor_5.0X11,199,793 - 11,199,917UniSTSRnor5.0
RGSC_v3.4X21,496,117 - 21,496,241UniSTSRGSC3.4
CeleraX10,012,325 - 10,012,449UniSTS
Cytogenetic MapXq12UniSTS
Ddx3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,481,644 - 9,481,917 (+)MAPPER
Rnor_6.0X10,402,476 - 10,402,748NCBIRnor6.0
Rnor_5.0X11,200,858 - 11,201,130UniSTSRnor5.0
RGSC_v3.4X21,497,182 - 21,497,454UniSTSRGSC3.4
CeleraX10,013,390 - 10,013,662UniSTS
Cytogenetic MapXq12UniSTS
DBX  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X116,167,281 - 116,167,369 (+)MAPPER
mRatBN7.2X9,479,848 - 9,479,935 (+)MAPPER
Rnor_6.0X123,538,974 - 123,539,061NCBIRnor6.0
Rnor_6.0X10,400,680 - 10,400,766NCBIRnor6.0
Rnor_5.0X123,683,915 - 123,684,002UniSTSRnor5.0
Rnor_5.0X11,199,062 - 11,199,148UniSTSRnor5.0
RGSC_v3.4X21,495,386 - 21,495,472UniSTSRGSC3.4
RGSC_v3.4X7,939,396 - 7,939,483UniSTSRGSC3.4
CeleraX115,397,167 - 115,397,254UniSTS
CeleraX10,011,594 - 10,011,680UniSTS
Cytogenetic MapXq12UniSTS
RH78345  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,480,580 - 9,480,704 (+)MAPPER
Rnor_6.0X10,401,412 - 10,401,535NCBIRnor6.0
Rnor_5.0X11,199,794 - 11,199,917UniSTSRnor5.0
RGSC_v3.4X21,496,118 - 21,496,241UniSTSRGSC3.4
CeleraX10,012,326 - 10,012,449UniSTS
Cytogenetic MapXq12UniSTS
RH127853  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,479,646 - 9,479,832 (+)MAPPER
Rnor_6.0X10,400,478 - 10,400,663NCBIRnor6.0
Rnor_5.0X11,198,860 - 11,199,045UniSTSRnor5.0
RGSC_v3.4X21,495,184 - 21,495,369UniSTSRGSC3.4
CeleraX10,011,392 - 10,011,577UniSTS
Cytogenetic MapXq12UniSTS
U42386  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,480,389 - 9,480,540 (+)MAPPER
Rnor_6.0X10,401,221 - 10,401,371NCBIRnor6.0
Rnor_5.0X11,199,603 - 11,199,753UniSTSRnor5.0
RGSC_v3.4X21,495,927 - 21,496,077UniSTSRGSC3.4
CeleraX10,012,135 - 10,012,285UniSTS
Cytogenetic MapXq12UniSTS
Ddx3x  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X9,481,040 - 9,481,952 (+)MAPPER
Rnor_6.0X10,401,872 - 10,402,783NCBIRnor6.0
Rnor_5.0X11,200,254 - 11,201,165UniSTSRnor5.0
RGSC_v3.4X21,496,578 - 21,497,489UniSTSRGSC3.4
CeleraX10,012,786 - 10,013,697UniSTS
Cytogenetic MapXq12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70166Bp65Blood pressure QTL 655.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166245312370298Rat
634325Bw13Body weight QTL 130body mass (VT:0001259)body weight (CMO:0000012)X166245321592783Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
631204Gluco15Glucose level QTL 150.001blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X183816624331837Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:557
Count of miRNA genes:275
Interacting mature miRNAs:356
Transcripts:ENSRNOT00000039551
Prediction methods:Miranda, Pita, 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.


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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000039551   ⟹   ENSRNOP00000029702
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX10,400,366 - 10,413,984 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091448   ⟹   ENSRNOP00000074025
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX10,402,725 - 10,413,995 (-)Ensembl
RefSeq Acc Id: NM_001108246   ⟹   NP_001101716
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,479,535 - 9,493,153 (-)NCBI
Rnor_6.0X10,400,366 - 10,413,984 (-)NCBI
Rnor_5.0X11,198,745 - 11,212,383 (-)NCBI
RGSC_v3.4X21,495,072 - 21,508,690 (-)RGD
CeleraX10,011,280 - 10,024,898 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256652   ⟹   XP_006256714
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,479,532 - 9,493,445 (-)NCBI
Rnor_6.0X10,400,363 - 10,414,010 (-)NCBI
Rnor_5.0X11,198,745 - 11,212,383 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006256653   ⟹   XP_006256715
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X9,479,597 - 9,493,455 (-)NCBI
Rnor_6.0X10,400,363 - 10,413,999 (-)NCBI
Rnor_5.0X11,198,745 - 11,212,383 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001101716 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256714 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256715 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL97652 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101716   ⟸   NM_001108246
- UniProtKB: D4ADE8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006256715   ⟸   XM_006256653
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006256714   ⟸   XM_006256652
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K719 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000074025   ⟸   ENSRNOT00000091448
RefSeq Acc Id: ENSRNOP00000029702   ⟸   ENSRNOT00000039551
Transcriptome

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

Promoters
RGD ID:13701711
Promoter ID:EPDNEW_R12229
Type:multiple initiation site
Name:Ddx3x_1
Description:DEAD-box helicase 3, X-linked
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_6.0X10,413,999 - 10,414,059EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 11203709 11203710 T A snv LE/OrlBarth (UDEL), Crl:SD (UDEL), IS/Kyo (KyushuU)
X 11204293 11204294 C A snv IS-Tlk/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 10404636 10404637 A G snv ACI/N (MCW)
X 10404675 10404676 C T snv M520/N (MCW), ACI/N (MCW)
X 10404714 10404715 C T snv Buf/N (MCW), WN/N (MCW)
X 10406152 10406153 C A snv Buf/N (MCW), WKY/N (MCW)
X 10407021 10407022 C T snv M520/N (MCW)
X 10407053 10407054 T C snv M520/N (MCW)
X 10407395 10407396 C A snv Buf/N (MCW), M520/N (MCW), WKY/N (MCW)
X 10407406 10407407 T C snv M520/N (MCW), WKY/N (MCW), Buf/N (MCW)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 21499398 21499399 T C snv FHL/EurMcwi (MCW)
X 21499420 21499421 C T snv BN/NHsdMcwi (KNAW), BUF/N (KNAW), WN/N (KNAW), SS/JrHsdMcwi (MCW), SHRSP/Gcrc (MDC), FHL/EurMcwi (MCW)
X 21499424 21499425 C T snv SS/JrHsdMcwi (MCW), FHL/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1564771 AgrOrtholog
Ensembl Genes ENSRNOG00000023383 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000029702 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000074025 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000039551 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000091448 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7107275 IMAGE-MGC_LOAD
InterPro DEAD/DEAH_box_helicase_dom UniProtKB/TrEMBL
  DNA/RNA_helicase_C UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  RNA-helicase_DEAD-box_CS UniProtKB/TrEMBL
  RNA_helicase_DEAD_Q_motif UniProtKB/TrEMBL
KEGG Report rno:317335 UniProtKB/TrEMBL
MGC_CLONE MGC:94798 IMAGE-MGC_LOAD
NCBI Gene 317335 ENTREZGENE
Pfam DEAD UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
PhenoGen Ddx3x 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 A0A0G2K719 ENTREZGENE, UniProtKB/TrEMBL
  D4ADE8 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Ddx3x  DEAD-box helicase 3, X-linked  Ddx3x  DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-08-01 Ddx3x  DEAD (Asp-Glu-Ala-Asp) box helicase 3, X-linked  Ddx3x  DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Ddx3x  DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked  Ddx3x  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Ddx3x  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 3, X-linked    DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked  Name updated 1299863 APPROVED
2006-02-09 Ddx3x  DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked      Symbol and Name status set to provisional 70820 PROVISIONAL