Human Gene DDX42 (ENST00000583590.5) Description and Page Index
  Description: ATP-dependent RNA helicase. Binds to partially double- stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm. (from UniProt Q86XP3)
RefSeq Summary (NM_203499): This gene encodes a member of the Asp-Glu-Ala-Asp (DEAD) box protein family. Members of this protein family are putative RNA helicases, and 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. Members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. Two transcript variants encoding the same protein have been identified for this gene. [provided by RefSeq, Jul 2008].
Gencode Transcript: ENST00000583590.5
Gencode Gene: ENSG00000198231.13
Transcript (Including UTRs)
   Position: hg38 chr17:63,773,884-63,819,317 Size: 45,434 Total Exon Count: 19 Strand: +
Coding Region
   Position: hg38 chr17:63,787,050-63,818,398 Size: 31,349 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsCTDRNA-Seq ExpressionMicroarray Expression
RNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA DescriptionsPathways
Other NamesMethods
Data last updated: 2019-09-04

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr17:63,773,884-63,819,317)mRNA (may differ from genome)Protein (938 aa)
Gene SorterGenome BrowserOther Species FASTAGene interactionsTable SchemaBioGPS
CGAPEnsemblExonPrimerGeneCardsHGNCHPRD
LynxMGIneXtProtPubMedReactomeStanford SOURCE
UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: DDX42_HUMAN
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase DDX42; EC=3.6.4.13; AltName: Full=DEAD box protein 42; AltName: Full=RNA helicase-like protein; Short=RHELP; AltName: Full=RNA helicase-related protein; Short=RNAHP; AltName: Full=SF3b DEAD box protein; AltName: Full=Splicing factor 3B-associated 125 kDa protein; Short=SF3b125;
FUNCTION: ATP-dependent RNA helicase. Binds to partially double- stranded RNAs (dsRNAs) in order to unwind RNA secondary structures. Unwinding is promoted in the presence of single-strand binding proteins. Mediates also RNA duplex formation thereby displacing the single-strand RNA binding protein. ATP and ADP modulate its activity: ATP binding and hydrolysis by DDX42 triggers RNA strand separation, whereas the ADP-bound form of the protein triggers annealing of complementary RNA strands. Involved in the survival of cells by interacting with TP53BP2 and thereby counteracting the apoptosis-stimulating activity of TP53BP2. Relocalizes TP53BP2 to the cytoplasm.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Component of splicing factor SF3B which is composed of at least eight subunits; SF3B1/SAP155/SF3B155, SF3B2/SAP145/SF3B155, SF3B3/SAP130/SF3B130, SF3B4/SAP49/SF3B49, SF3B14A, PHF5A/SF3B14B, SF3B10 and SF3B125. Interacts (via the C-terminus) with TP53BP2; the interaction is not inhibitied by TP53BP2 ubiquitination and is independent of p53/TP53.
SUBCELLULAR LOCATION: Cytoplasm. Nucleus speckle. Nucleus, Cajal body. Note=Isoform 2 is present in Cajal bodies (CBs) and nuclear speckles.
TISSUE SPECIFICITY: Expressed in several cell lines (at protein level). Expressed in liver, lung, tonsil, thymus, muscle and pancreatic islets.
SIMILARITY: Belongs to the DEAD box helicase family. DDX42 subfamily.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.
SEQUENCE CAUTION: Sequence=AAC32396.1; Type=Frameshift; Positions=818;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 42.00 RPKM in Ovary
Total median expression: 1544.79 RPKM



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

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -165.40412-0.401 Picture PostScript Text
3' UTR -273.20919-0.297 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 - DNA/RNA_helicase_DEAD/DEAH_N
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C
IPR000629 - RNA-helicase_DEAD-box_CS
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 Q86XP3
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-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
Genome BrowserGenome BrowserNo orthologNo orthologNo orthologNo ortholog
Gene Details     
Gene Sorter     
MGIRGD    
Protein SequenceProtein Sequence    
AlignmentAlignment    

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0003676 nucleic acid binding
GO:0003723 RNA binding
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity

Biological Process:
GO:0000398 mRNA splicing, via spliceosome
GO:0008104 protein localization
GO:0010501 RNA secondary structure unwinding
GO:0042981 regulation of apoptotic process

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0015030 Cajal body
GO:0016020 membrane
GO:0016607 nuclear speck


-  Descriptions from all associated GenBank mRNAs
  KF612910 - Homo sapiens MAP3K3/DDX42 fusion protein 1 mRNA, partial cds.
KF612911 - Homo sapiens MAP3K3/DDX42 fusion protein 2 mRNA, partial cds.
LF209396 - JP 2014500723-A/16899: Polycomb-Associated Non-Coding RNAs.
MA444973 - JP 2018138019-A/16899: Polycomb-Associated Non-Coding RNAs.
LF328268 - JP 2014500723-A/135771: Polycomb-Associated Non-Coding RNAs.
MA563845 - JP 2018138019-A/135771: Polycomb-Associated Non-Coding RNAs.
AK125169 - Homo sapiens cDNA FLJ43179 fis, clone FCBBF3013307, highly similar to Homo sapiens RNA helicase-related protein mRNA.
LF328269 - JP 2014500723-A/135772: Polycomb-Associated Non-Coding RNAs.
MA563846 - JP 2018138019-A/135772: Polycomb-Associated Non-Coding RNAs.
LP895346 - Sequence 210 from Patent EP3253886.
BC093081 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42, mRNA (cDNA clone MGC:111493 IMAGE:30407786), complete cds.
AB384900 - Synthetic construct DNA, clone: pF1KB4115, Homo sapiens DDX42 gene for ATP-dependent RNA helicase DDX42, complete cds, without stop codon, in Flexi system.
AB036090 - Homo sapiens mRNA for RNA helicase-related protein, complete cds.
BC015505 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42, mRNA (cDNA clone MGC:9119 IMAGE:3905607), complete cds.
DQ595300 - Homo sapiens piRNA piR-61412, complete sequence.
BC078667 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42, mRNA (cDNA clone IMAGE:6107393), partial cds.
AK292908 - Homo sapiens cDNA FLJ78746 complete cds, highly similar to Homo sapiens, RNA helicase-related protein.
LF328271 - JP 2014500723-A/135774: Polycomb-Associated Non-Coding RNAs.
MA563848 - JP 2018138019-A/135774: Polycomb-Associated Non-Coding RNAs.
AK095772 - Homo sapiens cDNA FLJ38453 fis, clone FEBRA2019663, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 (DDX42), transcript variant 2, mRNA.
AF083255 - Homo sapiens RNA helicase-related protein mRNA, complete cds.
CU677323 - Synthetic construct Homo sapiens gateway clone IMAGE:100017496 5' read DDX42 mRNA.
LF328272 - JP 2014500723-A/135775: Polycomb-Associated Non-Coding RNAs.
MA563849 - JP 2018138019-A/135775: Polycomb-Associated Non-Coding RNAs.
LF328276 - JP 2014500723-A/135779: Polycomb-Associated Non-Coding RNAs.
MA563853 - JP 2018138019-A/135779: Polycomb-Associated Non-Coding RNAs.
LF328277 - JP 2014500723-A/135780: Polycomb-Associated Non-Coding RNAs.
MA563854 - JP 2018138019-A/135780: Polycomb-Associated Non-Coding RNAs.
AK126480 - Homo sapiens cDNA FLJ44516 fis, clone UTERU3002600, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 (DDX42), transcript variant 2, mRNA.
LF328280 - JP 2014500723-A/135783: Polycomb-Associated Non-Coding RNAs.
MA563857 - JP 2018138019-A/135783: Polycomb-Associated Non-Coding RNAs.
AF147429 - Homo sapiens full length insert cDNA clone YP80G10.
LF328281 - JP 2014500723-A/135784: Polycomb-Associated Non-Coding RNAs.
MA563858 - JP 2018138019-A/135784: Polycomb-Associated Non-Coding RNAs.
AK122737 - Homo sapiens cDNA FLJ16253 fis, clone HLUNG2015184, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 (DDX42), transcript variant 2, mRNA.
AK001964 - Homo sapiens cDNA FLJ11102 fis, clone PLACE1005646, highly similar to Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 (DDX42), transcript variant 2, mRNA.
AL050096 - Homo sapiens mRNA; cDNA DKFZp586A0419 (from clone DKFZp586A0419).
LF328282 - JP 2014500723-A/135785: Polycomb-Associated Non-Coding RNAs.
MA563859 - JP 2018138019-A/135785: Polycomb-Associated Non-Coding RNAs.
AK096751 - Homo sapiens cDNA FLJ39432 fis, clone PROST2002927.
LF328283 - JP 2014500723-A/135786: Polycomb-Associated Non-Coding RNAs.
MA563860 - JP 2018138019-A/135786: Polycomb-Associated Non-Coding RNAs.
BC008208 - Homo sapiens DEAD (Asp-Glu-Ala-Asp) box polypeptide 42, mRNA (cDNA clone IMAGE:3869206), partial cds.
LF328284 - JP 2014500723-A/135787: Polycomb-Associated Non-Coding RNAs.
MA563861 - JP 2018138019-A/135787: Polycomb-Associated Non-Coding RNAs.
JD128643 - Sequence 109667 from Patent EP1572962.
JD068362 - Sequence 49386 from Patent EP1572962.
JD408731 - Sequence 389755 from Patent EP1572962.
LF328285 - JP 2014500723-A/135788: Polycomb-Associated Non-Coding RNAs.
MA563862 - JP 2018138019-A/135788: Polycomb-Associated Non-Coding RNAs.
JD442231 - Sequence 423255 from Patent EP1572962.
JD547096 - Sequence 528120 from Patent EP1572962.
LF328286 - JP 2014500723-A/135789: Polycomb-Associated Non-Coding RNAs.
MA563863 - JP 2018138019-A/135789: Polycomb-Associated Non-Coding RNAs.
JD286398 - Sequence 267422 from Patent EP1572962.
LF328287 - JP 2014500723-A/135790: Polycomb-Associated Non-Coding RNAs.
MA563864 - JP 2018138019-A/135790: Polycomb-Associated Non-Coding RNAs.
LF328288 - JP 2014500723-A/135791: Polycomb-Associated Non-Coding RNAs.
MA563865 - JP 2018138019-A/135791: Polycomb-Associated Non-Coding RNAs.
JD328908 - Sequence 309932 from Patent EP1572962.
LF328289 - JP 2014500723-A/135792: Polycomb-Associated Non-Coding RNAs.
MA563866 - JP 2018138019-A/135792: Polycomb-Associated Non-Coding RNAs.
JD439467 - Sequence 420491 from Patent EP1572962.
JD563679 - Sequence 544703 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  KEGG - Kyoto Encyclopedia of Genes and Genomes
hsa03040 - Spliceosome

Reactome (by CSHL, EBI, and GO)

Protein Q86XP3 (Reactome details) participates in the following event(s):

R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-75080 Formation of AT-AC A complex
R-HSA-75083 ATAC spliceosome mediated 3' splice site cleavage, exon ligation
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-75081 Formation of AT-AC B Complex
R-HSA-75082 ATAC spliceosome mediated Lariat formation,5' splice site cleavage
R-HSA-75079 Formation of AT-AC C complex
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-72165 mRNA Splicing - Minor Pathway
R-HSA-72172 mRNA Splicing
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-8953854 Metabolism of RNA

-  Other Names for This Gene
  Alternate Gene Symbols: A6NML1, A8KA43, DDX42_HUMAN, LP895346, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8, uc002jbv.1, uc002jbv.2, uc002jbv.3, uc002jbv.4, uc002jbv.5
UCSC ID: uc002jbv.5
RefSeq Accession: NM_203499
Protein: Q86XP3 (aka DDX42_HUMAN)
CCDS: CCDS32704.1

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