DDX39B (DExD-box helicase 39B) - Rat Genome Database

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Gene: DDX39B (DExD-box helicase 39B) Canis lupus familiaris
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Symbol: DDX39B
Name: DExD-box helicase 39B
RGD ID: 12113861
Description: ENCODES a protein that exhibits ATP-dependent activity, acting on RNA (ortholog); ATP-dependent protein binding (ortholog); identical protein binding (ortholog); INVOLVED IN liver development (ortholog); positive regulation of cell growth involved in cardiac muscle cell development (ortholog); positive regulation of DNA biosynthetic process (ortholog); PARTICIPATES IN NXF1-NXT1 export pathway; spliceosome pathway; ASSOCIATED WITH genetic disease (ortholog); megacolon (ortholog); Neurodevelopmental Disorders (ortholog); FOUND IN nuclear matrix (ortholog); protein-containing complex (ortholog); transcription export complex (ortholog)
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 56 kDa U2AF65-associated protein; BAT1; DEAD box protein UAP56; DEAD-box helicase 39B; HLA-B associated transcript 1; spliceosome RNA helicase BAT1; spliceosome RNA helicase DDX39B; UAP56
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12692158   PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
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
(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
(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
(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
(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
180 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 5 5 22 6 6 6 6 6 12 8 10 6
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSCAFT00000036511   ⟹   ENSCAFP00000031897
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl121,032,368 - 1,044,492 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845018143   ⟹   ENSCAFP00845014141
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl121,176,147 - 1,189,567 (-)Ensembl
RefSeq Acc Id: ENSCAFT00845018184   ⟹   ENSCAFP00845014175
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl121,178,188 - 1,190,041 (-)Ensembl
RefSeq Acc Id: NM_001014377   ⟹   NP_001014399
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1121,032,598 - 1,042,994 (-)NCBI
Dog10K_Boxer_Tasha121,169,048 - 1,179,440 (-)NCBI
ROS_Cfam_1.0121,177,831 - 1,188,229 (-)NCBI
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
Sequence:
RefSeq Acc Id: XM_038682711   ⟹   XP_038538639
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0121,177,608 - 1,189,698 (-)NCBI
RefSeq Acc Id: XM_038682712   ⟹   XP_038538640
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0121,177,608 - 1,189,705 (-)NCBI
RefSeq Acc Id: XM_038682713   ⟹   XP_038538641
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0121,177,608 - 1,189,703 (-)NCBI
RefSeq Acc Id: NP_001014399   ⟸   NM_001014377
- UniProtKB: Q5WR10 (UniProtKB/Swiss-Prot),   A0A8C0L8B6 (UniProtKB/TrEMBL),   A0A8I3NE94 (UniProtKB/TrEMBL),   A0A8P0SPY2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000031897   ⟸   ENSCAFT00000036511
RefSeq Acc Id: XP_038538640   ⟸   XM_038682712
- Peptide Label: isoform X2
- UniProtKB: Q5WR10 (UniProtKB/Swiss-Prot),   A0A8C0L8B6 (UniProtKB/TrEMBL),   A0A8I3NE94 (UniProtKB/TrEMBL),   A0A8P0SPY2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038538641   ⟸   XM_038682713
- Peptide Label: isoform X2
- UniProtKB: Q5WR10 (UniProtKB/Swiss-Prot),   A0A8C0L8B6 (UniProtKB/TrEMBL),   A0A8I3NE94 (UniProtKB/TrEMBL),   A0A8P0SPY2 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038538639   ⟸   XM_038682711
- Peptide Label: isoform X1
- UniProtKB: A0A8I3NE94 (UniProtKB/TrEMBL),   A0A8P0SPY2 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845014175   ⟸   ENSCAFT00845018184
RefSeq Acc Id: ENSCAFP00845014141   ⟸   ENSCAFT00845018143
Promoters
RGD ID:13685336
Promoter ID:EPDNEW_C3405
Type:single initiation site
Name:DDX39B_2
Description:DExD-box helicase 39B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_C3406  
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1121,043,090 - 1,043,150EPDNEW
RGD ID:13685337
Promoter ID:EPDNEW_C3406
Type:multiple initiation site
Name:DDX39B_1
Description:DExD-box helicase 39B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_C3405  
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1121,044,366 - 1,044,426EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000000509 Ensembl, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENSCAFG00030004350 UniProtKB/Swiss-Prot
  ENSCAFG00040009227 UniProtKB/Swiss-Prot
  ENSCAFG00805013926 UniProtKB/Swiss-Prot
  ENSCAFG00845010305 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000036511.4 UniProtKB/TrEMBL
  ENSCAFT00000095917.1 UniProtKB/Swiss-Prot
  ENSCAFT00030008005.1 UniProtKB/Swiss-Prot
  ENSCAFT00040017081.1 UniProtKB/Swiss-Prot
  ENSCAFT00805025297 UniProtKB/Swiss-Prot
  ENSCAFT00845018143 ENTREZGENE
  ENSCAFT00845018143.1 UniProtKB/Swiss-Prot
  ENSCAFT00845018184.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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 cfa:474839 UniProtKB/Swiss-Prot
NCBI Gene DDX39B 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
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 A0A8C0L8B6 ENTREZGENE
  A0A8I3NE94 ENTREZGENE, UniProtKB/TrEMBL
  A0A8P0SPY2 ENTREZGENE, UniProtKB/TrEMBL
  DX39B_CANLF UniProtKB/Swiss-Prot, ENTREZGENE
VGNC ID VGNC:39855 ENTREZGENE