Ddx21 (DExD-box helicase 21) - Rat Genome Database

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Gene: Ddx21 (DExD-box helicase 21) Rattus norvegicus
Analyze
Symbol: Ddx21
Name: DExD-box helicase 21
RGD ID: 1307306
Description: Predicted to have RNA binding activity; RNA helicase activity; and identical protein binding activity. Predicted to be involved in several processes, including cellular macromolecule biosynthetic process; positive regulation of I-kappaB kinase/NF-kappaB signaling; and positive regulation of myeloid dendritic cell cytokine production. Predicted to localize to chromosome; cytosol; and nuclear lumen. Orthologous to human DDX21 (DExD-box helicase 21); INTERACTS WITH (+)-schisandrin B; 2,4-dinitrotoluene; 2,6-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: Ddx21a; Ddx21b; DEAD (Asp-Glu-Ala-Asp) box helicase 21; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a; DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b; DEAD box protein 21; DEAD-box helicase 21; gu-alpha; LOC317399; LOC361847; MGC112658; MGC124980; nucleolar RNA helicase 2; nucleolar RNA helicase Gu; nucleolar RNA helicase II; RH II/Gu
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
mRatBN7.22030,534,319 - 30,554,513 (-)NCBI
Rnor_6.0 Ensembl2032,213,148 - 32,232,632 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02032,213,147 - 32,232,632 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02033,997,711 - 34,017,196 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,838,671 - 29,860,514 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2031,953,138 - 31,973,565 (-)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(+)-schisandrin B  (EXP)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,2',4,4'-Tetrabromodiphenyl ether  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-nitrofluorene  (EXP)
3H-1,2-dithiole-3-thione  (EXP)
4-(N-nitrosomethylamino)-1-(3-pyridyl)butan-1-one  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
afimoxifene  (ISO)
aflatoxin B1  (EXP,ISO)
all-trans-retinoic acid  (ISO)
amphetamine  (EXP)
antirheumatic drug  (ISO)
arsenous acid  (ISO)
belinostat  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bisphenol A  (EXP,ISO)
carbon nanotube  (ISO)
chloropicrin  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibric acid  (EXP)
cobalt dichloride  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
cyclosporin A  (ISO)
deoxynivalenol  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (EXP)
dioxygen  (ISO)
enzyme inhibitor  (ISO)
flutamide  (EXP)
fulvestrant  (ISO)
furan  (ISO)
gentamycin  (EXP)
leflunomide  (ISO)
lipopolysaccharide  (ISO)
lithium atom  (EXP)
lithium hydride  (EXP)
methamphetamine  (EXP)
methapyrilene  (EXP)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
N-methyl-4-phenylpyridinium  (ISO)
N-nitrosodiethylamine  (EXP)
N-nitrosodimethylamine  (EXP)
nefazodone  (EXP)
nickel atom  (ISO)
ochratoxin A  (ISO)
paracetamol  (EXP)
pentachlorophenol  (ISO)
perfluorononanoic acid  (ISO)
perfluorooctanoic acid  (EXP)
phenobarbital  (EXP)
piperonyl butoxide  (EXP)
pirinixic acid  (EXP,ISO)
potassium dichromate  (ISO)
pregnenolone 16alpha-carbonitrile  (ISO)
progesterone  (ISO)
propiconazole  (ISO)
raloxifene  (ISO)
resveratrol  (EXP,ISO)
rotenone  (EXP)
sodium dichromate  (EXP)
sunitinib  (ISO)
tamibarotene  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
trimellitic anhydride  (ISO)
triphenyl phosphate  (EXP)
tungsten  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vinclozolin  (EXP)
zinc dichloride  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromosome  (ISO)
cytosol  (ISO,ISS)
mitochondrion  (IEA)
nucleolus  (IBA,ISO,ISS)
nucleoplasm  (ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:1639225   PMID:9461305   PMID:12477932   PMID:15489334   PMID:16210410   PMID:19946888   PMID:21703541   PMID:22658674   PMID:22681889   PMID:25470060   PMID:28431233   PMID:28790157  


Genomics

Comparative Map Data
Ddx21
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22030,534,319 - 30,554,513 (-)NCBI
Rnor_6.0 Ensembl2032,213,148 - 32,232,632 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02032,213,147 - 32,232,632 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02033,997,711 - 34,017,196 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42029,838,671 - 29,860,514 (-)NCBIRGSC3.4rn4RGSC3.4
Celera2031,953,138 - 31,973,565 (-)NCBICelera
Cytogenetic Map20q11NCBI
DDX21
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1068,956,170 - 68,985,068 (+)EnsemblGRCh38hg38GRCh38
GRCh381068,956,131 - 68,985,068 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371070,715,926 - 70,744,824 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361070,385,898 - 70,414,285 (+)NCBINCBI36hg18NCBI36
Build 341070,385,897 - 70,414,285NCBI
Celera1063,991,762 - 64,020,150 (+)NCBI
Cytogenetic Map10q22.1NCBI
HuRef1064,717,792 - 64,746,685 (+)NCBIHuRef
CHM1_11070,997,606 - 71,026,553 (+)NCBICHM1_1
Ddx21
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391062,416,026 - 62,438,077 (-)NCBIGRCm39mm39
GRCm39 Ensembl1062,416,030 - 62,438,060 (-)Ensembl
GRCm381062,580,247 - 62,602,298 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1062,580,251 - 62,602,281 (-)EnsemblGRCm38mm10GRCm38
MGSCv371062,042,995 - 62,065,046 (-)NCBIGRCm37mm9NCBIm37
MGSCv361061,975,604 - 61,997,655 (-)NCBImm8
Celera1063,683,725 - 63,705,771 (-)NCBICelera
Cytogenetic Map10B4NCBI
cM Map1032.43NCBI
Ddx21
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543722,050,937 - 22,071,118 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543722,050,029 - 22,071,213 (-)NCBIChiLan1.0ChiLan1.0
DDX21
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11067,956,857 - 67,985,867 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1067,956,857 - 67,985,867 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01065,423,319 - 65,452,266 (+)NCBIMhudiblu_PPA_v0panPan3
DDX21
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1420,109,719 - 20,134,586 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl420,109,778 - 20,132,338 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha420,240,134 - 20,264,990 (+)NCBI
ROS_Cfam_1.0420,381,832 - 20,407,325 (+)NCBI
UMICH_Zoey_3.1420,282,539 - 20,307,462 (+)NCBI
UNSW_CanFamBas_1.0420,485,654 - 20,510,665 (+)NCBI
UU_Cfam_GSD_1.0420,828,776 - 20,854,073 (+)NCBI
Ddx21
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721360,933,799 - 60,956,220 (-)NCBI
SpeTri2.0NW_0049365219,426,544 - 9,448,973 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX21
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1472,039,996 - 72,063,720 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11472,039,985 - 72,063,778 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21478,054,874 - 78,078,395 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DDX21
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1962,339,614 - 62,370,032 (-)NCBI
Ddx21
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247543,180,501 - 3,203,449 (+)NCBI

Position Markers
BI302095  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02032,232,789 - 32,232,941NCBIRnor6.0
Rnor_5.02034,017,353 - 34,017,505UniSTSRnor5.0
RGSC_v3.42029,860,671 - 29,860,823UniSTSRGSC3.4
Celera2031,973,722 - 31,973,874UniSTS
RH 3.4 Map20308.38UniSTS
Cytogenetic Map20q11UniSTS
RH129516  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map20q11UniSTS
RH133206  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02032,214,507 - 32,214,687NCBIRnor6.0
Rnor_6.0X19,383,535 - 19,383,715NCBIRnor6.0
Rnor_5.02033,999,071 - 33,999,251UniSTSRnor5.0
Rnor_5.0X20,150,411 - 20,150,591UniSTSRnor5.0
RGSC_v3.42029,840,031 - 29,840,211UniSTSRGSC3.4
RGSC_v3.4X38,742,330 - 38,742,510UniSTSRGSC3.4
CeleraX18,831,612 - 18,831,792UniSTS
Celera2031,954,498 - 31,954,678UniSTS
Cytogenetic Map20q11UniSTS
RH144150  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.02032,225,948 - 32,226,109NCBIRnor6.0
Rnor_5.02034,010,512 - 34,010,673UniSTSRnor5.0
RGSC_v3.42029,852,037 - 29,852,198UniSTSRGSC3.4
Celera2031,966,539 - 31,966,700UniSTS
RH 3.4 Map20308.36UniSTS
Cytogenetic Map20q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201782709656205956Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201887215049108956Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)202085847056205956Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202660884356205956Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202660884356205956Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202660884356205956Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202671232356205956Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)203091348156205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:901
Count of miRNA genes:320
Interacting mature miRNAs:429
Transcripts:ENSRNOT00000068184
Prediction methods:Microtar, Miranda, 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 40 55 39 19 39 8 10 74 35 36 11 8
Low 3 2 2 2 1 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068184   ⟹   ENSRNOP00000063494
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2032,213,148 - 32,232,632 (-)Ensembl
RefSeq Acc Id: NM_001037201   ⟹   NP_001032278
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22030,534,319 - 30,554,513 (-)NCBI
Rnor_6.02032,213,147 - 32,232,632 (-)NCBI
Rnor_5.02033,997,711 - 34,017,196 (-)NCBI
RGSC_v3.42029,838,671 - 29,860,514 (-)RGD
Celera2031,953,138 - 31,973,565 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001032278 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI05879 (Get FASTA)   NCBI Sequence Viewer  
  EDL92965 (Get FASTA)   NCBI Sequence Viewer  
  Q3B8Q1 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001032278   ⟸   NM_001037201
- UniProtKB: Q3B8Q1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000063494   ⟸   ENSRNOT00000068184
Transcriptome

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

Promoters
RGD ID:13701616
Promoter ID:EPDNEW_R12140
Type:multiple initiation site
Name:Ddx21_1
Description:DExD-box helicase 21
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_6.02032,232,644 - 32,232,704EPDNEW

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)
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)
FHH/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
FHL/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)
FHL/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
GH/OmrMcwi (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)
GK/Ox (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
LE/Stm (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
LEW/Crl (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
LEW/NCrlBR (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
LH/MavRrrc (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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307306 AgrOrtholog
Ensembl Genes ENSRNOG00000043099 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000063494 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000068184 ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7126328 IMAGE-MGC_LOAD
InterPro DEAD/DEAH_box_helicase_dom UniProtKB/Swiss-Prot
  GUCT UniProtKB/Swiss-Prot
  Helicase_ATP-bd UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RNA_helicase_DEAD_Q_motif UniProtKB/Swiss-Prot
KEGG Report rno:317399 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124980 IMAGE-MGC_LOAD
NCBI Gene 317399 ENTREZGENE
Pfam DEAD UniProtKB/Swiss-Prot
  GUCT UniProtKB/Swiss-Prot
  Helicase_C UniProtKB/Swiss-Prot
PhenoGen Ddx21 PhenoGen
PROSITE HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot
  HELICASE_CTER UniProtKB/Swiss-Prot
  Q_MOTIF UniProtKB/Swiss-Prot
SMART DEXDc UniProtKB/Swiss-Prot
  HELICc UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
  SSF54928 UniProtKB/Swiss-Prot
UniProt DDX21_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-05 Ddx21  DExD-box helicase 21  Ddx21  DEAD-box helicase 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-13 Ddx21  DEAD-box helicase 21  Ddx21  DEAD (Asp-Glu-Ala-Asp) box helicase 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-11-04 Ddx21  DEAD (Asp-Glu-Ala-Asp) box helicase 21  Ddx21b  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b  Data Merged 737654 APPROVED
2012-07-16 Ddx21  DEAD (Asp-Glu-Ala-Asp) box helicase 21  Ddx21  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-03 Ddx21  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21  Ddx21a  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Ddx21b  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b  Ddx21b_predicted  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b (predicted)  Symbol and Name updated 1559027 APPROVED
2005-12-06 Ddx21a  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a  Ddx21a_predicted  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Ddx21a_predicted  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21a (predicted)      Symbol and Name status set to approved 70820 APPROVED
2005-01-12 Ddx21b_predicted  DEAD (Asp-Glu-Ala-Asp) box polypeptide 21b (predicted)      Symbol and Name status set to approved 70820 APPROVED