Ddx39b (DExD-box helicase 39B) - Rat Genome Database

Send us a Message



 Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) RatMine GViewer (Genome Viewer) Overgo Probe Designer VCMap
Aging & Age-Related Disease Cancer Cardiovascular Disease COVID-19 Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models   new Genetic Models Autism Models PhenoMiner (Quantitative Phenotypes) Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes GERRC (Gene Editing Rat Resource Center) Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Poster Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Gene: Ddx39b (DExD-box helicase 39B) Rattus norvegicus
Analyze
Symbol: Ddx39b
Name: DExD-box helicase 39B
RGD ID: 70923
Description: Predicted to enable several functions, including ATP hydrolysis activity; ATP-dependent protein binding activity; and snRNA binding activity. Involved in several processes, including positive regulation of cell growth involved in cardiac muscle cell development; positive regulation of macromolecule biosynthetic process; and positive regulation of vascular associated smooth muscle cell proliferation. Located in nuclear matrix. Part of protein-containing complex. Human ortholog(s) of this gene implicated in type 1 diabetes mellitus. Orthologous to human DDX39B (DExD-box helicase 39B); PARTICIPATES IN NXF1-NXT1 export pathway; spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 3-chloropropane-1,2-diol.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 56 kDa U2AF65-associated protein; ATP-dependent RNA helicase p47; Bat1; Bat1a; D17H6S81E-1; D20H6S81e; DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B; DEAD box protein UAP56; DEAD-box helicase 39B; DNA segment Chr 17 human D6S81E 1; HLA-B associated transcript 1; HLA-B associated transcript 1A; HLA-B-associated transcript 1A; Nuclear RNA helicase; p47; spliceosome RNA helicase Bat1; spliceosome RNA helicase Ddx39b
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,547,702 - 3,585,064 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl203,572,056 - 3,584,996 (-)Ensembl
Rnor_6.0204,806,103 - 4,818,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,806,108 - 4,818,568 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,886,503 - 6,898,979 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,611,128 - 3,623,578 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,611,355 - 3,623,754 (-)NCBI
Celera204,440,470 - 4,452,912 (+)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (ISO)
2,4-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
2-hydroxypropanoic acid  (ISO)
3-chloropropane-1,2-diol  (EXP)
4-amino-2,6-dinitrotoluene  (EXP)
5-fluorouracil  (ISO)
7,12-dimethyltetraphene  (EXP)
aconitine  (EXP)
ammonium chloride  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
benzo[a]pyrene  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
calcium dichloride  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP)
copper atom  (EXP)
copper(0)  (EXP)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glyphosate  (EXP)
isoflavones  (EXP)
ivermectin  (ISO)
lead diacetate  (ISO)
nickel atom  (EXP)
nickel sulfate  (EXP)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
phenobarbital  (ISO)
rac-lactic acid  (ISO)
SB 431542  (ISO)
selenium atom  (ISO)
sodium arsenite  (ISO)
sodium fluoride  (ISO)
temozolomide  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
trichloroethene  (EXP)
trichostatin A  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
1. Chang TH, etal., Biochim Biophys Acta. 2013 Aug;1829(8):764-74. doi: 10.1016/j.bbagrm.2013.02.006. Epub 2013 Feb 21.
2. Cheong KY, etal., Hum Immunol. 2001 Dec;62(12):1363-70.
3. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. GOA data from the GO Consortium
5. Gohshi T, etal., J Biochem. 1999 May;125(5):939-46.
6. Helou K, etal., Hereditas 1999;130(2):105-9.
7. Katahira J Biochim Biophys Acta. 2012 Jun;1819(6):507-13. doi: 10.1016/j.bbagrm.2011.12.001. Epub 2011 Dec 8.
8. Kwak JO, etal., J Nephrol. 2005 Nov-Dec;18(6):681-9.
9. Lambracht-Washington D and Fischer Lindahl K, Immunogenetics 2002 Mar;53(12):1039-46.
10. MGD Curation, June 12, 2002
11. MGD data from the GO Consortium
12. Nair S, etal., J Biol Chem 1992 Jun 25;267(18):12928-35.
13. Price P, etal., Hum Mol Genet. 2004 May 1;13(9):967-74. Epub 2004 Mar 17.
14. RGD automated data pipeline
15. RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. RGD automated import pipeline for gene-chemical interactions
17. Sahni A, etal., Biochem Biophys Res Commun. 2010 Feb 26;393(1):106-10. doi: 10.1016/j.bbrc.2010.01.093. Epub 2010 Jan 29.
18. Sahni A, etal., Biochem Biophys Res Commun. 2012 Apr 13;420(3):511-5. doi: 10.1016/j.bbrc.2012.03.022. Epub 2012 Mar 13.
19. Sahni A, etal., Biochem Biophys Res Commun. 2013 Feb 15;431(3):636-40. doi: 10.1016/j.bbrc.2012.12.014. Epub 2012 Dec 12.
20. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:14667819   PMID:15047853   PMID:15489334   PMID:15833825   PMID:15998806   PMID:17190602   PMID:17562711   PMID:18593880   PMID:18974867   PMID:20844015   PMID:21859714   PMID:22082260  
PMID:22144908   PMID:22658674   PMID:22681889   PMID:25145264  


Genomics

Comparative Map Data
Ddx39b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2203,547,702 - 3,585,064 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl203,572,056 - 3,584,996 (-)Ensembl
Rnor_6.0204,806,103 - 4,818,600 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl204,806,108 - 4,818,568 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0206,886,503 - 6,898,979 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4203,611,128 - 3,623,578 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1203,611,355 - 3,623,754 (-)NCBI
Celera204,440,470 - 4,452,912 (+)NCBICelera
Cytogenetic Map20p12NCBI
DDX39B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38631,530,226 - 31,542,003 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl631,530,219 - 31,542,448 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,498,003 - 31,509,780 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,605,975 - 31,618,204 (-)NCBINCBI36hg18NCBI36
Build 34631,605,974 - 31,617,904NCBI
Celera633,096,234 - 33,108,459 (-)NCBI
Cytogenetic Map6p21.33NCBI
HuRef631,284,705 - 31,296,997 (-)NCBIHuRef
CHM1_1631,500,137 - 31,512,390 (-)NCBICHM1_1
T2T-CHM13v2.0631,383,322 - 31,395,095 (-)NCBI
Ddx39b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,460,722 - 35,472,683 (+)NCBIGRCm39mm39
GRCm39 Ensembl1735,460,722 - 35,472,683 (+)Ensembl
GRCm381735,241,746 - 35,253,707 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,241,746 - 35,253,707 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,378,691 - 35,390,652 (+)NCBIGRCm37mm9NCBIm37
MGSCv361734,355,767 - 34,367,554 (+)NCBImm8
MGSCv361734,849,922 - 34,861,736 (+)NCBImm8
Celera1738,343,889 - 38,346,696 (+)NCBICelera
Cytogenetic Map17B1NCBI
cM Map1718.6NCBI
Ddx39b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543772,835 - 84,384 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543772,835 - 84,045 (-)NCBIChiLan1.0ChiLan1.0
DDX39B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1632,081,210 - 32,093,135 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,081,210 - 32,092,569 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0631,191,333 - 31,203,246 (-)NCBIMhudiblu_PPA_v0panPan3
DDX39B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1121,032,377 - 1,044,465 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl121,032,368 - 1,044,492 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha121,169,048 - 1,179,440 (-)NCBI
ROS_Cfam_1.0121,177,608 - 1,189,705 (-)NCBI
ROS_Cfam_1.0 Ensembl121,176,147 - 1,190,041 (-)Ensembl
UMICH_Zoey_3.1121,036,642 - 1,047,031 (-)NCBI
UNSW_CanFamBas_1.0121,104,617 - 1,114,937 (-)NCBI
UU_Cfam_GSD_1.0121,171,204 - 1,181,685 (-)NCBI
Ddx39b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,580,562 - 35,597,123 (-)NCBI
SpeTri2.0NW_0049367271,968,032 - 1,980,789 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX39B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,658,086 - 23,673,083 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1723,658,089 - 23,669,095 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2727,582,945 - 27,593,980 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DDX39B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11740,445,258 - 40,457,379 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl1740,447,061 - 40,456,826 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604431,430,956 - 31,442,672 (-)NCBIVero_WHO_p1.0
Ddx39b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475424,657,914 - 24,667,579 (+)EnsemblHetGla_female_1.0hetGla2
HetGla 1.0NW_00462475424,657,019 - 24,667,225 (+)NCBIHetGla_female_1.0hetGla2

Position Markers
D20Yum47  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,576,110 - 3,576,337 (+)MAPPERmRatBN7.2
Rnor_6.0204,809,696 - 4,809,922NCBIRnor6.0
Rnor_5.0206,890,096 - 6,890,322UniSTSRnor5.0
RGSC_v3.4203,614,716 - 3,614,942UniSTSRGSC3.4
Celera204,449,105 - 4,449,331UniSTS
Cytogenetic Map20p12UniSTS
Bat1_microsatellite  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,572,729 - 3,572,876 (+)MAPPERmRatBN7.2
Rnor_6.0204,806,315 - 4,806,461NCBIRnor6.0
Rnor_5.0206,886,715 - 6,886,861UniSTSRnor5.0
RGSC_v3.4203,611,335 - 3,611,481UniSTSRGSC3.4
Celera204,452,559 - 4,452,705UniSTS
Cytogenetic Map20p12UniSTS
RH144334  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,572,601 - 3,572,969 (+)MAPPERmRatBN7.2
Rnor_6.0204,806,187 - 4,806,554NCBIRnor6.0
Rnor_5.0206,886,587 - 6,886,954UniSTSRnor5.0
RGSC_v3.4203,611,207 - 3,611,574UniSTSRGSC3.4
Celera204,452,466 - 4,452,833UniSTS
RH 3.4 Map2050.5UniSTS
Cytogenetic Map20p12UniSTS
RH126881  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2203,572,569 - 3,572,935 (+)MAPPERmRatBN7.2
Rnor_6.0204,806,155 - 4,806,520NCBIRnor6.0
Rnor_5.0206,886,555 - 6,886,920UniSTSRnor5.0
RGSC_v3.4203,611,175 - 3,611,540UniSTSRGSC3.4
Celera204,452,500 - 4,452,865UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724519Bp144Blood pressure QTL 1440.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)2013624629Rat
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124159021Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125159026Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20127339237Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20129191651Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20129191651Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20129191651Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20129191651Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20129191651Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
2306850Pia40Pristane induced arthritis QTL 400.0001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2015279595304575Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
61448Ciaa1CIA Autoantibody QTL 1300.001blood autoantibody amount (VT:0003725)calculated serum anti-rat type 2 collagen autoantibody titer (CMO:0001281)2026463954597031Rat
61472Aia1Adjuvant induced arthritis QTL 1180.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)2026463954597031Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20289259726381954Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:132
Count of miRNA genes:109
Interacting mature miRNAs:114
Transcripts:ENSRNOT00000001115
Prediction methods:Microtar, 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 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001115   ⟹   ENSRNOP00000001115
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,572,523 - 3,584,996 (-)Ensembl
Rnor_6.0 Ensembl204,806,108 - 4,818,568 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000077809
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,572,410 - 3,584,996 (-)Ensembl
Rnor_6.0 Ensembl204,809,903 - 4,818,539 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000080174   ⟹   ENSRNOP00000075517
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,572,527 - 3,583,591 (-)Ensembl
Rnor_6.0 Ensembl204,806,108 - 4,817,146 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,807,028 - 4,809,785 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087615
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,806,327 - 4,808,119 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116798   ⟹   ENSRNOP00000093667
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl203,572,056 - 3,584,996 (-)Ensembl
RefSeq Acc Id: NM_133300   ⟹   NP_579834
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,572,523 - 3,584,973 (-)NCBI
Rnor_6.0204,806,108 - 4,818,558 (-)NCBI
Rnor_5.0206,886,503 - 6,898,979 (-)NCBI
RGSC_v3.4203,611,128 - 3,623,578 (-)RGD
Celera204,440,470 - 4,452,912 (+)RGD
Sequence:
RefSeq Acc Id: XM_039098378   ⟹   XP_038954306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,547,702 - 3,585,063 (-)NCBI
RefSeq Acc Id: XR_005497163
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,572,519 - 3,583,971 (-)NCBI
RefSeq Acc Id: XR_005497165
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,547,702 - 3,585,064 (-)NCBI
RefSeq Acc Id: XR_362030
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2203,572,519 - 3,585,064 (-)NCBI
Rnor_6.0204,806,103 - 4,818,600 (-)NCBI
Rnor_5.0206,886,503 - 6,898,979 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_579834   ⟸   NM_133300
- UniProtKB: Q63413 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075517   ⟸   ENSRNOT00000080174
RefSeq Acc Id: ENSRNOP00000001115   ⟸   ENSRNOT00000001115
RefSeq Acc Id: XP_038954306   ⟸   XM_039098378
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000093667   ⟸   ENSRNOT00000116798
Protein Domains
Helicase ATP-binding   Helicase C-terminal   Q_MOTIF

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q63413-F1-model_v2 AlphaFold Q63413 1-428 view protein structure

Transcriptome

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

Promoters
RGD ID:13701365
Promoter ID:EPDNEW_R11888
Type:initiation region
Name:Ddx39b_1
Description:DExD-box helicase 39B
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_6.0204,818,524 - 4,818,584EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: RGSC_v3.4
Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
20 3611341 3611342 C T snv ACI/EurMcwi (MCW), COP/CrCrl (MCW & UW), FHH/EurMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:70923 AgrOrtholog
BioCyc Gene G2FUF-4670 BioCyc
Ensembl Genes ENSRNOG00000000841 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000001115 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000075517 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000001115 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000080174 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7100155 IMAGE-MGC_LOAD
InterPro DEAD/DEAH_box_helicase_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_ATP-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RNA_helicase_DEAD_Q_motif UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:114612 UniProtKB/Swiss-Prot
MGC_CLONE MGC:91440 IMAGE-MGC_LOAD
NCBI Gene 114612 ENTREZGENE
Pfam DEAD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Helicase_C UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ddx39b PhenoGen
PROSITE HELICASE_ATP_BIND_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICASE_CTER UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Q_MOTIF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART DEXDc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HELICc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2KAT4_RAT UniProtKB/TrEMBL
  DX39B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q811A6 UniProtKB/Swiss-Prot
  Q8R2G9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-10-05 Ddx39b  DExD-box helicase 39B  Ddx39b  DEAD-box helicase 39B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-01-13 Ddx39b  DEAD-box helicase 39B  Ddx39b  DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-28 Ddx39b  DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B  Bat1  HLA-B associated transcript 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-25 Bat1  HLA-B associated transcript 1  Bat1a  HLA-B-associated transcript 1A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2003-04-09 Bat1a  HLA-B-associated transcript 1A      Symbol and Name updated 629477 APPROVED
2003-03-11 Bat1a  HLA-B-associated transcript 1A  D20H6S81e  Nuclear RNA helicase  Data Merged 628472 PROVISIONAL
2002-07-09 Bat1a  HLA-B-associated transcript 1A      Symbol and Name updated to reflect Human and Mouse nomenclature 70877 APPROVED
2002-06-10 D20H6S81e  Nuclear RNA helicase      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression mRNA expression in liver is cell cycle dependent and developmentally regulated 632224
gene_other the start of the MHC class I region downstrean of the rat Bat1a gene contains a sequence with similarity to intron 3 of the mouse H-2D gene but without the coding region 632223