Ddx31 (DEAD-box helicase 31) - Rat Genome Database
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Gene: Ddx31 (DEAD-box helicase 31) Rattus norvegicus
Analyze
Symbol: Ddx31
Name: DEAD-box helicase 31
RGD ID: 1304895
Description: Predicted to have ATP binding activity; RNA binding activity; and RNA helicase activity. Predicted to be involved in ribosome biogenesis. Predicted to localize to Golgi apparatus and nucleolus. Orthologous to human DDX31 (DEAD-box helicase 31); INTERACTS WITH (+)-schisandrin B; 2,4,6-trinitrotoluene; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: DEAD (Asp-Glu-Ala-Asp) box polypeptide 31; DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31; LOC311835; probable ATP-dependent RNA helicase DDX31
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
mRatBN7.2312,172,829 - 12,238,392 (+)NCBI
Rnor_6.0 Ensembl37,422,820 - 7,488,617 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.037,422,871 - 7,488,299 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0312,773,068 - 12,838,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,849,554 - 7,914,005 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,849,651 - 7,914,732 (+)NCBI
Celera36,952,740 - 7,017,059 (+)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:12477932   PMID:22658674   PMID:22681889   PMID:23019224  


Genomics

Comparative Map Data
Ddx31
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2312,172,829 - 12,238,392 (+)NCBI
Rnor_6.0 Ensembl37,422,820 - 7,488,617 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.037,422,871 - 7,488,299 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0312,773,068 - 12,838,525 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.437,849,554 - 7,914,005 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.137,849,651 - 7,914,732 (+)NCBI
Celera36,952,740 - 7,017,059 (+)NCBICelera
Cytogenetic Map3p12NCBI
DDX31
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl9132,592,997 - 132,670,401 (-)EnsemblGRCh38hg38GRCh38
GRCh389132,592,997 - 132,670,401 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh379135,468,384 - 135,545,788 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369134,459,497 - 134,535,609 (-)NCBINCBI36hg18NCBI36
Build 349132,542,803 - 132,575,342NCBI
Celera9106,011,427 - 106,087,527 (-)NCBI
Cytogenetic Map9q34.13NCBI
HuRef9104,963,490 - 105,039,530 (-)NCBIHuRef
CHM1_19135,618,757 - 135,696,158 (-)NCBICHM1_1
Ddx31
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39228,730,418 - 28,795,587 (+)NCBIGRCm39mm39
GRCm39 Ensembl228,730,418 - 28,795,583 (+)Ensembl
GRCm38228,840,406 - 28,905,575 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl228,840,406 - 28,905,571 (+)EnsemblGRCm38mm10GRCm38
MGSCv37228,695,926 - 28,761,095 (+)NCBIGRCm37mm9NCBIm37
MGSCv36228,662,746 - 28,727,579 (+)NCBImm8
Celera228,546,305 - 28,611,439 (+)NCBICelera
Cytogenetic Map2A3NCBI
Ddx31
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555131,970,830 - 2,031,908 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555131,970,386 - 2,036,572 (-)NCBIChiLan1.0ChiLan1.0
DDX31
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.19132,297,226 - 132,418,713 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9132,341,965 - 132,418,713 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v09103,665,553 - 103,787,705 (-)NCBIMhudiblu_PPA_v0panPan3
DDX31
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1951,631,608 - 51,700,747 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl951,629,757 - 51,699,301 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha950,896,296 - 50,965,808 (+)NCBI
ROS_Cfam_1.0952,524,554 - 52,594,192 (+)NCBI
UMICH_Zoey_3.1951,304,543 - 51,374,091 (+)NCBI
UNSW_CanFamBas_1.0951,629,079 - 51,698,570 (+)NCBI
UU_Cfam_GSD_1.0951,708,706 - 51,778,277 (+)NCBI
Ddx31
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_ltri_2NW_024404947199,353,677 - 199,412,484 (-)NCBI
SpeTri2.0NW_00493648719,123,422 - 19,179,285 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX31
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1272,383,595 - 272,454,198 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11272,383,585 - 272,454,395 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21306,415,843 - 306,486,509 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DDX31
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1125,468,127 - 5,545,610 (+)NCBI
ChlSab1.1 Ensembl125,468,412 - 5,549,120 (+)Ensembl
Ddx31
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247603,692,248 - 3,763,887 (+)NCBI

Position Markers
WI-20657  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.037,466,959 - 7,467,208NCBIRnor6.0
Rnor_5.0312,817,185 - 12,817,434UniSTSRnor5.0
RGSC_v3.437,893,566 - 7,893,815UniSTSRGSC3.4
Celera36,996,620 - 6,996,869UniSTS
Cytogenetic Map3p12UniSTS
RH133179  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.037,487,174 - 7,487,354NCBIRnor6.0
Rnor_5.0312,837,400 - 12,837,580UniSTSRnor5.0
RGSC_v3.437,913,782 - 7,913,962UniSTSRGSC3.4
Celera37,016,836 - 7,017,016UniSTS
Cytogenetic Map3p12UniSTS
BE119836  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.037,488,101 - 7,488,255NCBIRnor6.0
Rnor_5.0312,838,327 - 12,838,481UniSTSRnor5.0
RGSC_v3.437,914,709 - 7,914,863UniSTSRGSC3.4
Celera37,017,763 - 7,017,917UniSTS
RH 3.4 Map333.4UniSTS
Cytogenetic Map3p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)3600074851687917Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)3600074851687917Rat
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3128136884Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3328592928136884Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3128500807Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3128500807Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3125786001Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3139773425Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3263142133477544Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3128500807Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3132972944Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)3600086634394121Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)3600086634394121Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3195176874Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3328592928136884Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3137891710Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)3600074834394365Rat
8693641Alc30Alcohol consumption QTL 3020.739drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)3565463925105730Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3263142148562146Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:74
Count of miRNA genes:58
Interacting mature miRNAs:68
Transcripts:ENSRNOT00000064323
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.


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 12 4 14 4 6 6 29 1
Low 3 43 45 37 5 37 8 11 68 29 12 10 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000064323   ⟹   ENSRNOP00000061319
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl37,422,820 - 7,488,617 (+)Ensembl
RefSeq Acc Id: NM_001107824   ⟹   NP_001101294
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,173,032 - 12,237,490 (+)NCBI
Rnor_6.037,423,086 - 7,487,397 (+)NCBI
Rnor_5.0312,773,068 - 12,838,525 (+)NCBI
RGSC_v3.437,849,554 - 7,914,005 (+)RGD
Celera36,952,740 - 7,017,059 (+)RGD
Sequence:
RefSeq Acc Id: XM_006233799   ⟹   XP_006233861
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.037,422,874 - 7,488,299 (+)NCBI
Rnor_5.0312,773,068 - 12,838,525 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017591828   ⟹   XP_017447317
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.037,422,871 - 7,462,956 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039105223   ⟹   XP_038961151
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2312,172,829 - 12,238,392 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101294 (Get FASTA)   NCBI Sequence Viewer  
  XP_038961151 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI60917 (Get FASTA)   NCBI Sequence Viewer  
  EDL93395 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001101294   ⟸   NM_001107824
- UniProtKB: B1H297 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006233861   ⟸   XM_006233799
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447317   ⟸   XM_017591828
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000061319   ⟸   ENSRNOT00000064323
RefSeq Acc Id: XP_038961151   ⟸   XM_039105223
- Peptide Label: isoform X1
Transcriptome

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

Promoters
RGD ID:13691939
Promoter ID:EPDNEW_R2464
Type:single initiation site
Name:Ddx31_1
Description:DEAD-box helicase 31
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_6.037,422,872 - 7,422,932EPDNEW

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)
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
LN/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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
SBH/Ygl (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: 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
3 12837179 12837180 G A snv SHR/NCrlPrin (KNAW), SHR/NHsd (KNAW), SHR/OlaIpcv (KNAW), SHR/OlaIpcvPrin (KNAW), SHRSP/Gcrc (KNAW), DOB/Oda (KyushuU), WKY/N (KNAW), WKY/NCrl (KNAW), WKY/NHsd (KNAW), IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), WKY/Gcrc (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
3 7486953 7486954 G A snv WKY/N (MCW), SHR/NHsd (RGD), WKY/NHsd (RGD), WKY/NCrl (RGD), WKY/Gcrc (RGD), SHRSP/Gcrc (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1304895 AgrOrtholog
Ensembl Genes ENSRNOG00000013040 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000061319 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064323 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7457829 IMAGE-MGC_LOAD
InterPro DEAD-like_helicase UniProtKB/TrEMBL
  DNA/RNA_helicase_DEAD/DEAH_N UniProtKB/TrEMBL
  DUF4217 UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  RNA-helicase_DEAD-box_CS UniProtKB/TrEMBL
  RNA_helicase_DEAD_Q_motif UniProtKB/TrEMBL
KEGG Report rno:311835 UniProtKB/TrEMBL
MGC_CLONE MGC:188660 IMAGE-MGC_LOAD
NCBI Gene 311835 ENTREZGENE
Pfam DEAD UniProtKB/TrEMBL
  DUF4217 UniProtKB/TrEMBL
  Helicase_C UniProtKB/TrEMBL
PhenoGen Ddx31 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
  DUF4217 UniProtKB/TrEMBL
  HELICc UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt B1H297 ENTREZGENE, UniProtKB/TrEMBL
  G3V9V8_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-13 Ddx31  DEAD-box helicase 31  Ddx31  DEAD (Asp-Glu-Ala-Asp) box polypeptide 31  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Ddx31  DEAD (Asp-Glu-Ala-Asp) box polypeptide 31  Ddx31  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ddx31  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31   Ddx31_predicted  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ddx31_predicted  DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 31 (predicted)      Symbol and Name status set to approved 70820 APPROVED