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

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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 RNA 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 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
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 Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8203,577,200 - 3,589,651 (-)NCBIGRCr8
mRatBN7.2203,547,702 - 3,585,064 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,572,056 - 3,584,996 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,272,550 - 4,284,961 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,634,613 - 3,647,024 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,172,085 - 4,184,507 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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->4)-beta-D-glucan  (ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (ISO)
17beta-estradiol  (EXP)
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)
bisphenol F  (ISO)
caffeine  (ISO)
calcium dichloride  (ISO)
carbon nanotube  (ISO)
chlordecone  (ISO)
chlorpyrifos  (EXP,ISO)
copper atom  (EXP)
copper(0)  (EXP)
coumestrol  (ISO)
Cuprizon  (EXP)
cyclosporin A  (ISO)
diarsenic trioxide  (ISO)
Dibutyl phosphate  (ISO)
dibutyl phthalate  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
elemental selenium  (ISO)
Enterolactone  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenthion  (ISO)
flutamide  (EXP)
folic acid  (ISO)
gentamycin  (EXP)
glafenine  (EXP)
glyphosate  (EXP)
isoflavones  (EXP)
ivermectin  (ISO)
lead diacetate  (ISO)
methidathion  (ISO)
nickel atom  (EXP)
nickel sulfate  (EXP)
paracetamol  (EXP,ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (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)
triphenyl phosphate  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
vanadyl sulfate  (ISO)
vinclozolin  (EXP)
vitamin E  (ISO)
vorinostat  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Functions of the DExD/H-box proteins in nuclear pre-mRNA splicing. 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. Localization of central MHC genes influencing type I diabetes. Cheong KY, etal., Hum Immunol. 2001 Dec;62(12):1363-70.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Molecular cloning of mouse p47, a second group mammalian RuvB DNA helicase-like protein: homology with those from human and Saccharomyces cerevisiae. Gohshi T, etal., J Biochem. 1999 May;125(5):939-46.
6. Cytogenetic localization of the growth and reproduction complex (Grc) in the rat and in the mouse and its position in relation to RT1.EC and other loci in the rat MHC. Helou K, etal., Hereditas 1999;130(2):105-9.
7. mRNA export and the TREX complex. Katahira J Biochim Biophys Acta. 2012 Jun;1819(6):507-13. doi: 10.1016/j.bbagrm.2011.12.001. Epub 2011 Dec 8.
8. Co-localization and interaction of b0,+-type amino acid transporter 1 (BAT1) with caveolin-1 in rat kidney. Kwak JO, etal., J Nephrol. 2005 Nov-Dec;18(6):681-9.
9. Does the rat have an H2-D orthologue next to Bat1? Lambracht-Washington D and Fischer Lindahl K, Immunogenetics 2002 Mar;53(12):1039-46.
10. Gene Data Set MGD Curation, June 12, 2002
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. Molecular cloning and analysis of an eIF-4A-related rat liver nuclear protein. Nair S, etal., J Biol Chem 1992 Jun 25;267(18):12928-35.
13. Polymorphisms at positions -22 and -348 in the promoter of the BAT1 gene affect transcription and the binding of nuclear factors. Price P, etal., Hum Mol Genet. 2004 May 1;13(9):967-74. Epub 2004 Mar 17.
14. GOA pipeline RGD automated data pipeline
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. UAP56 is an important regulator of protein synthesis and growth in cardiomyocytes. 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. UAP56 is a novel interacting partner of Bcr in regulating vascular smooth muscle cell DNA synthesis. 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. UAP56 is an important mediator of angiotensin II/platelet derived growth factor induced vascular smooth muscle cell DNA synthesis and proliferation. 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. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. 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
GRCr8203,577,200 - 3,589,651 (-)NCBIGRCr8
mRatBN7.2203,547,702 - 3,585,064 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl203,572,056 - 3,584,996 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx204,272,550 - 4,284,961 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0203,634,613 - 3,647,024 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0204,172,085 - 4,184,507 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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.p14 Ensembl631,530,219 - 31,542,448 (-)EnsemblGRCh38hg38GRCh38
GRCh37631,498,003 - 31,509,780 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36631,605,975 - 31,618,204 (-)NCBINCBI36Build 36hg18NCBI36
Build 34631,605,974 - 31,617,904NCBI
Celera633,096,234 - 33,108,459 (-)NCBICelera
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 (-)NCBIT2T-CHM13v2.0
Ddx39b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391735,460,722 - 35,472,683 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1735,460,722 - 35,472,683 (+)EnsemblGRCm39 Ensembl
GRCm381735,241,746 - 35,253,707 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1735,241,746 - 35,253,707 (+)EnsemblGRCm38mm10GRCm38
MGSCv371735,378,691 - 35,390,652 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361734,355,767 - 34,367,554 (+)NCBIMGSCv36mm8
MGSCv361734,849,922 - 34,861,736 (+)NCBIMGSCv36mm8
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
NHGRI_mPanPan1-v2546,007,204 - 46,019,088 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1641,968,724 - 41,980,648 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0631,191,333 - 31,203,246 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1632,081,210 - 32,093,135 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl632,081,210 - 32,092,569 (-)Ensemblpanpan1.1panPan2
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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0121,177,608 - 1,189,705 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl121,176,147 - 1,190,041 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1121,036,642 - 1,047,031 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0121,104,617 - 1,114,937 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0121,171,204 - 1,181,685 (-)NCBIUU_Cfam_GSD_1.0
Ddx39b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494635,580,562 - 35,597,123 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367271,968,094 - 1,980,785 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367271,968,032 - 1,980,789 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DDX39B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl723,658,088 - 23,670,031 (-)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 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1740,447,061 - 40,456,826 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604431,430,956 - 31,442,672 (-)NCBIVero_WHO_p1.0Vero_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_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475424,657,019 - 24,667,225 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ddx39b
2467 total Variants
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.


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

Markers in Region
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


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


RefSeq Acc Id: ENSRNOT00000001115   ⟹   ENSRNOP00000001115
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
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
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
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,807,028 - 4,809,785 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000087615
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl204,806,327 - 4,808,119 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000116798   ⟹   ENSRNOP00000093667
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
GRCr8203,577,201 - 3,589,651 (-)NCBI
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_063278929   ⟹   XP_063134999
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8203,577,200 - 3,589,586 (-)NCBI
RefSeq Acc Id: NP_579834   ⟸   NM_133300
- UniProtKB: Q811A6 (UniProtKB/Swiss-Prot),   Q8R2G9 (UniProtKB/Swiss-Prot),   Q63413 (UniProtKB/Swiss-Prot),   A6KTX4 (UniProtKB/TrEMBL),   A0A8I6A103 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075517   ⟸   ENSRNOT00000080174
RefSeq Acc Id: ENSRNOP00000001115   ⟸   ENSRNOT00000001115
RefSeq Acc Id: ENSRNOP00000093667   ⟸   ENSRNOT00000116798
RefSeq Acc Id: XP_063134999   ⟸   XM_063278929
- Peptide Label: isoform X1
- UniProtKB: Q8R2G9 (UniProtKB/Swiss-Prot),   Q811A6 (UniProtKB/Swiss-Prot),   Q63413 (UniProtKB/Swiss-Prot),   A0A8I6A103 (UniProtKB/TrEMBL),   A6KTX4 (UniProtKB/TrEMBL)
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

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
  ENSRNOG00055007825 UniProtKB/Swiss-Prot
  ENSRNOG00060003574 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001115 ENTREZGENE
  ENSRNOT00000001115.7 UniProtKB/Swiss-Prot
  ENSRNOT00000077809.2 UniProtKB/TrEMBL
  ENSRNOT00000080174.2 UniProtKB/TrEMBL
  ENSRNOT00000116798.1 UniProtKB/TrEMBL
  ENSRNOT00055013130 UniProtKB/Swiss-Prot
  ENSRNOT00060005855 UniProtKB/Swiss-Prot
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, UniProtKB/TrEMBL
MGC_CLONE MGC:91440 IMAGE-MGC_LOAD
NCBI Gene 114612 ENTREZGENE
PANTHER ATP-DEPENDENT RNA HELICASE DBP3 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SPLICEOSOME RNA HELICASE DDX39B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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
RatGTEx ENSRNOG00000000841 RatGTEx
  ENSRNOG00055007825 RatGTEx
  ENSRNOG00060003574 RatGTEx
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
  A0A8I6A103 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AKU4_RAT UniProtKB/TrEMBL
  A6KTX4 ENTREZGENE, UniProtKB/TrEMBL
  DX39B_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q811A6 ENTREZGENE
  Q8R2G9 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 from RGD:2485 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