Human Gene DDX39A (ENST00000242776.9_6) from GENCODE V45lift37
  Description: Homo sapiens DExD-box helicase 39A (DDX39A), transcript variant 1, mRNA. (from RefSeq NM_005804)
RefSeq Summary (NM_005804): This gene encodes a member of the DEAD box protein family. These proteins are characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD) and are putative RNA helicases. They are implicated in a number of cellular processes involving alteration of RNA secondary structure, such as translation initiation, nuclear and mitochondrial splicing, and ribosome and spliceosome assembly. Based on their distribution patterns, some members of the DEAD box protein family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. This gene is thought to play a role in the prognosis of patients with gastrointestinal stromal tumors. A pseudogene of this gene is present on chromosome 13. Alternate splicing results in multiple transcript variants. Additional alternatively spliced transcript variants of this gene have been described, but their full-length nature is not known. [provided by RefSeq, Sep 2013].
Gencode Transcript: ENST00000242776.9_6
Gencode Gene: ENSG00000123136.15_9
Transcript (Including UTRs)
   Position: hg19 chr19:14,519,610-14,530,153 Size: 10,544 Total Exon Count: 11 Strand: -
Coding Region
   Position: hg19 chr19:14,519,748-14,524,032 Size: 4,285 Coding Exon Count: 10 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureGO Annotations
mRNA DescriptionsPathwaysOther NamesMethods
Data last updated at UCSC: 2024-04-24 11:59:55

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr19:14,519,610-14,530,153)mRNA (may differ from genome)Protein (427 aa)
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-  Comments and Description Text from UniProtKB
  ID: DX39A_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase DDX39A; EC=3.6.4.13; AltName: Full=DEAD box protein 39; AltName: Full=Nuclear RNA helicase URH49;
FUNCTION: [Isoform 1]: Involved in pre-mRNA splicing. Required for the export of mRNA out of the nucleus.
CATALYTIC ACTIVITY: Reaction=ATP + H2O = ADP + H(+) + phosphate; Xref=Rhea:RHEA:13065, ChEBI:CHEBI:15377, ChEBI:CHEBI:15378, ChEBI:CHEBI:30616, ChEBI:CHEBI:43474, ChEBI:CHEBI:456216; EC=3.6.4.13;
SUBUNIT: Binds ALYREF/THOC4 and DDX39B/BAT1. Interacts with SARNP. Interacts with human cytomegalovirus/HHV-5 protein UL69. Interacts with MX1. Interacts with MCM3AP isoform GANP (PubMed:23652018).
INTERACTION: O00148; Q9Y3Y2-3: CHTOP; NbExp=3; IntAct=EBI-348253, EBI-11984237; O00148; O00148: DDX39A; NbExp=4; IntAct=EBI-348253, EBI-348253; O00148; Q13838: DDX39B; NbExp=4; IntAct=EBI-348253, EBI-348622; O00148; P04792: HSPB1; NbExp=3; IntAct=EBI-348253, EBI-352682; O00148; P42858: HTT; NbExp=3; IntAct=EBI-348253, EBI-466029; O00148; P78317: RNF4; NbExp=3; IntAct=EBI-348253, EBI-2340927; O00148; P82979: SARNP; NbExp=4; IntAct=EBI-348253, EBI-347495; O00148; P21673: SAT1; NbExp=3; IntAct=EBI-348253, EBI-711613; O00148; P54274: TERF1; NbExp=2; IntAct=EBI-348253, EBI-710997; O00148; Q7KZS0: UBE2I; NbExp=3; IntAct=EBI-348253, EBI-10180829; O00148; O76024: WFS1; NbExp=3; IntAct=EBI-348253, EBI-720609; O00148; H0YHG0; NbExp=3; IntAct=EBI-348253, EBI-6190012;
SUBCELLULAR LOCATION: Nucleus Cytoplasm Note=Can translocate to the cytoplasm in the presence of MX1.
TISSUE SPECIFICITY: Detected in testis, and at lower levels in brain, kidney, lung, thymus, spleen and salivary gland.
INDUCTION: Up-regulated in proliferating cells. Present at low levels in quiescent cells.
MISCELLANEOUS: [Isoform 2]: Probably devoid of RNA helicase activity.
MISCELLANEOUS: [Isoform 3]: Probably devoid of RNA helicase activity.
SIMILARITY: Belongs to the DEAD box helicase family. DECD subfamily.
SEQUENCE CAUTION: Sequence=BAB15509.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence=;

-  Primer design for this transcript
 

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Click here to load the transcript sequence and exon structure into Primer3Plus

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Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: DDX39A
Diseases sorted by gene-association score: gastrointestinal stromal tumor (3), inflammatory bowel disease 6 (2)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 126.51 RPKM in Testis
Total median expression: 966.81 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -20.1076-0.264 Picture PostScript Text
3' UTR -27.40138-0.199 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011545 - DEAD/DEAH_box_helicase_dom
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR027417 - P-loop_NTPase
IPR014014 - RNA_helicase_DEAD_Q_motif

Pfam Domains:
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain

ModBase Predicted Comparative 3D Structure on O00148
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-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATPase activity
GO:0042802 identical protein binding

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0006397 mRNA processing
GO:0006405 RNA export from nucleus
GO:0006406 mRNA export from nucleus
GO:0008380 RNA splicing
GO:0031124 mRNA 3'-end processing

Cellular Component:
GO:0000346 transcription export complex
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005737 cytoplasm
GO:0016020 membrane
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  AL512698 - Homo sapiens mRNA; cDNA DKFZp547B159 (from clone DKFZp547B159).
AK026614 - Homo sapiens cDNA: FLJ22961 fis, clone KAT10214.
BC001009 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 39, mRNA (cDNA clone MGC:8417 IMAGE:2820926), complete cds.
BC032128 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 39, mRNA (cDNA clone MGC:29546 IMAGE:5017293), complete cds.
BC010455 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 39, mRNA (cDNA clone IMAGE:4155840), with apparent retained intron.
AK301847 - Homo sapiens cDNA FLJ55484 complete cds, highly similar to ATP-dependent RNA helicase DDX39 (EC 3.6.1.-).
U90426 - Human nuclear RNA helicase, complete cds.
JD055091 - Sequence 36115 from Patent EP1572962.
JD522530 - Sequence 503554 from Patent EP1572962.
KJ892962 - Synthetic construct Homo sapiens clone ccsbBroadEn_02356 DDX39A gene, encodes complete protein.
DQ891387 - Synthetic construct clone IMAGE:100004017; FLH176433.01X; RZPDo839D03122D DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 (DDX39) gene, encodes complete protein.
DQ894563 - Synthetic construct Homo sapiens clone IMAGE:100009023; FLH176432.01L; RZPDo839D03121D DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 (DDX39) gene, encodes complete protein.
JD185987 - Sequence 167011 from Patent EP1572962.
JD143141 - Sequence 124165 from Patent EP1572962.
JD460909 - Sequence 441933 from Patent EP1572962.
KJ902076 - Synthetic construct Homo sapiens clone ccsbBroadEn_11470 DDX39A gene, encodes complete protein.
CU689284 - Synthetic construct Homo sapiens gateway clone IMAGE:100021890 5' read DDX39 mRNA.
JD482328 - Sequence 463352 from Patent EP1572962.
JD534536 - Sequence 515560 from Patent EP1572962.
JD386121 - Sequence 367145 from Patent EP1572962.
JD150545 - Sequence 131569 from Patent EP1572962.
JD187427 - Sequence 168451 from Patent EP1572962.
AB254849 - Homo sapiens DDX39 mRNA for DEAD (Asp-Glu-Ala-Asp) box polypeptide 39 transcript variant, complete cds.
KJ902077 - Synthetic construct Homo sapiens clone ccsbBroadEn_11471 DDX39A gene, encodes complete protein.
CU679723 - Synthetic construct Homo sapiens gateway clone IMAGE:100023448 5' read DDX39 mRNA.
CU674496 - Synthetic construct Homo sapiens gateway clone IMAGE:100017246 5' read DDX39 mRNA.
AK293911 - Homo sapiens cDNA FLJ59857 complete cds, moderately similar to ATP-dependent RNA helicase DDX39 (EC 3.6.1.-).
JD022808 - Sequence 3832 from Patent EP1572962.
JD031729 - Sequence 12753 from Patent EP1572962.
JD023759 - Sequence 4783 from Patent EP1572962.
JD030529 - Sequence 11553 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein O00148 (Reactome details) participates in the following event(s):

R-HSA-8849157 TREX complex binds spliced, capped mRNA:CBC:EJC cotranscriptionally
R-HSA-159101 NXF1:NXT1 (TAP:p15) binds capped mRNA:CBC:EJC:TREX (minus DDX39B)
R-HSA-72185 mRNA polyadenylation
R-HSA-72180 Cleavage of mRNA at the 3'-end
R-HSA-72187 mRNA 3'-end processing
R-HSA-159236 Transport of Mature mRNA derived from an Intron-Containing Transcript
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-72202 Transport of Mature Transcript to Cytoplasm
R-HSA-8953854 Metabolism of RNA
R-HSA-109688 Cleavage of Growing Transcript in the Termination Region
R-HSA-73856 RNA Polymerase II Transcription Termination
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-74160 Gene expression (Transcription)

-  Other Names for This Gene
  Alternate Gene Symbols: DDX39, DX39A_HUMAN, ENST00000242776.1, ENST00000242776.2, ENST00000242776.3, ENST00000242776.4, ENST00000242776.5, ENST00000242776.6, ENST00000242776.7, ENST00000242776.8, NM_005804, O00148, Q9BVP6, Q9H5W0, uc317ekt.1
UCSC ID: ENST00000242776.9_6
RefSeq Accession: NM_005804
Protein: O00148 (aka DX39A_HUMAN)

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.