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DDX42 Gene

protein-coding   GIFtS: 51
GCID: GC17P061851

DEAD (Asp-Glu-Ala-Asp) Box Helicase 42

(Previous name: DEAD (Asp-Glu-Ala-Asp) box polypeptide 42)
  See related diseases
at  

(According to 1HGNC, 2Entrez Gene,
3UniProtKB/Swiss-Prot, 4UniProtKB/TrEMBL, 5OMIM, 6GeneLoc, 7Ensembl, 8DME, 9miRBase, 10fRNAdb, 12H-InvDB, 13NCBI, 14NONCODE, and/or 15RNAdb)
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Aliases
DEAD (Asp-Glu-Ala-Asp) Box Helicase 421 2     DDX42P2
RHELP2 3 5     SF3B82
DEAD (Asp-Glu-Ala-Asp) Box Polypeptide 421 2     ATP-Dependent RNA Helicase DDX422
Splicing Factor 3B-Associated 125 KDa Protein2 3     Splicing Factor 3b, Subunit 82
RNAHP2 3     EC 3.6.4.133
SF3b1252 3     DEAD Box Protein 423
SF3b DEAD Box Protein2 3     RNA Helicase-Like Protein3
Splicing Factor 3b1     RNA Helicase-Related Protein3
Subunit 81     EC 3.6.18

External Ids:    HGNC: 186761   Entrez Gene: 113252   Ensembl: ENSG000001982317   OMIM: 6133695   UniProtKB: Q86XP33   

Export aliases for DDX42 gene to outside databases

Previous GC identifers: GC17P062192 GC17P062337 GC17P059205 GC17P057219


(According to Entrez Gene, GeneCards, Tocris Bioscience, Wikipedia's Gene Wiki, PharmGKB,
UniProtKB/Swiss-Prot, and/or UniProtKB/TrEMBL)
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Entrez Gene summary for DDX42 Gene:
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)

GeneCards Summary for DDX42 Gene:
DDX42 (DEAD (Asp-Glu-Ala-Asp) box helicase 42) is a protein-coding gene. Diseases associated with DDX42 include japanese encephalitis, and encephalitis. GO annotations related to this gene include RNA binding and ATP-dependent helicase activity. An important paralog of this gene is DDX46.

UniProtKB/Swiss-Prot: DDX42_HUMAN, Q86XP3
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

Gene Wiki entry for DDX42 Gene


(According to GeneLoc and/or HGNC, and/or
Entrez Gene (NCBI build 37),
and/or miRBase,
Genomic Views according to UCSC (hg19) and Ensembl (release 75), Regulatory elements and Epigenetics data according to QIAGEN, and/or SwitchGear Genomics)
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Regulatory elements:
   Regulatory transcription factor binding sites in the DDX42 gene promoter:
         TBP   GR   Elk-1   AML1a   GR-beta   AREB6   HNF-1   GR-alpha   LyF-1   
         Other transcription factors

SwitchGear Promoter luciferase reporter plasmidDDX42 promoter sequence
   Search Chromatin IP Primers for DDX42

Epigenetics:
DNA Methylation CpG Assay Predesigned for Pyrosequencing in human, mouse, rat DDX42


Genomic Location:
Genomic View: UCSC Golden Path with GeneCards custom track

Entrez Gene cytogenetic band: 17q23.3   Ensembl cytogenetic band:  17q23.3   HGNC cytogenetic band: 17q23

DDX42 Gene in genomic location: bands according to Ensembl, locations according to (and/or Entrez Gene and/or Ensembl if different)
DDX42 gene location

GeneLoc information about chromosome 17         GeneLoc Exon Structure

GeneLoc location for GC17P061851:  view genomic region     (about GC identifiers)

Start:
61,850,963 bp from pter      End:
61,896,677 bp from pter
Size:
45,715 bases      Orientation:
plus strand

(According to 1UniProtKB, HORDE, 2neXtProt, Ensembl, and/or Reactome, Modification sites according to PhosphoSitePlus, Specific Peptides from DME, RefSeq according to NCBI, PDB rendering according to OCA and/or Proteopedia, Recombinant Proteins from EMD Millipore, R&D Systems, GenScript, Enzo Life Sciences, OriGene, Novus Biologicals, Sino Biological, ProSpec, and/or Cloud-Clone Corp.,
Biochemical Assays by EMD Millipore, R&D Systems, OriGene, GenScript, Cell Signaling Technology, Enzo Life Sciences, and/or Cloud-Clone Corp., Antibodies by EMD Millipore, R&D Systems, Cell Signaling Technology, OriGene, Novus Biologicals, Thermo Fisher Scientific, LSBio, Abcam, and/or Cloud-Clone Corp.)
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UniProtKB/Swiss-Prot: DDX42_HUMAN, Q86XP3 (See protein sequence)
Recommended Name: ATP-dependent RNA helicase DDX42  
Size: 938 amino acids; 102975 Da
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
Sequence caution: Sequence=AAC32396.1; Type=Frameshift; Positions=818;
Secondary accessions: A6NML1 A8KA43 O75619 Q68G51 Q96BK1 Q96HR7 Q9Y3V8
Alternative splicing: 2 isoforms:  Q86XP3-1   Q86XP3-2   

Explore the universe of human proteins at neXtProt for DDX42: NX_Q86XP3

Explore proteomics data for DDX42 at MOPED

Post-translational modifications: 

  • Modification sites at neXtProt
  • Modification sites at PhosphoSitePlus
  • Selected DME Specific Peptides for DDX42 (Q86XP3) (see all 30)
     AFQSQYK  GAMGDRL  QSERNKV  TPGRLID 


    See DDX42 Protein Expression from SPIRE MOPED, PaxDB, and MaxQB

    REFSEQ proteins (2 alternative transcripts): 
    NP_031398.2  NP_987095.1  

    ENSEMBL proteins: 
     ENSP00000464232   ENSP00000464050   ENSP00000463561   ENSP00000352308   ENSP00000463038  
     ENSP00000462174   ENSP00000461957   ENSP00000374574   ENSP00000390121  

    DDX42 Human Recombinant Protein Products:

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    Novus Biologicals DDX42 Protein
    Novus Biologicals DDX42 Lysates
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    Browse Sino Biological Cell Lysates
    Browse ProSpec Recombinant Proteins
    Cloud-Clone Corp. Proteins for DDX42

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    DDX42 Assay Products:

    Browse Kits and Assays available from EMD Millipore
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    Cloud-Clone Corp. ELISAs for DDX42
    Cloud-Clone Corp. CLIAs for DDX42


    (According to HGNC, IUPHAR, InterPro, ProtoNet, UniProtKB, and/or BLOCKS, Sets of similar genes according to GeneDecks)
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    HGNC Gene Families:
    DDX: DEAD-boxes

    Selected InterPro protein domains (see all 6):
     IPR011545 DNA/RNA_helicase_DEAD/DEAH_N
     IPR000629 RNA-helicase_DEAD-box_CS
     IPR027417 P-loop_NTPase
     IPR014014 RNA_helicase_DEAD_Q_motif
     IPR014001 Helicase_ATP-bd

    Graphical View of Domain Structure for InterPro Entry Q86XP3

    ProtoNet protein and cluster: Q86XP3

    1 Blocks protein domain: IPB000629 ATP-dependent helicase

    UniProtKB/Swiss-Prot: DDX42_HUMAN, Q86XP3
    Similarity: Belongs to the DEAD box helicase family. DDX42 subfamily
    Similarity: Contains 1 helicase ATP-binding domain
    Similarity: Contains 1 helicase C-terminal domain


    DDX42 for domains           About GeneDecksing


    (According to 1UniProtKB, Genatlas, LifeMap Discovery™, IUBMB, and/or 2DME, Human phenotypes from GenomeRNAi, Animal models from MGI Mar 06 2013, inGenious Targeting Laboratory, genOway,
    transcription factor targeting from QIAGEN and/or HOMER, miRNA Gene Targets from miRTarBase, shRNA from OriGene, siRNAs from OriGene, QIAGEN, microRNA from QIAGEN, SwitchGear Genomics, Gene Editing from DNA2.0, Clones from OriGene, GenScript, Sino Biological, DNA2.0, and Vector BioLabs, Cell Lines from GenScript, ESI BIO, In Situ Hybridization Assays from Advanced Cell Diagnostics, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Molecular Function:

         UniProtKB/Swiss-Prot Summary: DDX42_HUMAN, Q86XP3
    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

         Enzyme Numbers (IUBMB): EC 3.6.12 EC 3.6.4.131

         Gene Ontology (GO): Selected molecular function terms (see all 7):    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0003676nucleic acid binding ----
    GO:0003723RNA binding ----
    GO:0004386helicase activity ----
    GO:0005515protein binding IPI19377511
    GO:0005524ATP binding IEA--
         
    DDX42 for ontologies           About GeneDecksing


    Phenotypes:
         3 GenomeRNAi human phenotypes for DDX42:
     Increased gamma-H2AX phosphory  Low eccentricity cells  Synthetic lethal with Ras 

    Animal Models:
       inGenious Targeting Laboratory: Let us create your new Knockout/Knockin mouse model for DDX42
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    miRNA
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    miRTarBase miRNAs that target DDX42:
    hsa-mir-1 (MIRT023974), hsa-mir-10a-5p (MIRT047595), hsa-mir-99a-5p (MIRT048682), hsa-mir-186-5p (MIRT045158), hsa-mir-345-5p (MIRT042731), hsa-mir-615-3p (MIRT040200)

    Block miRNA regulation of human, mouse, rat DDX42 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DDX42 (see all 19):
    hsa-miR-549 hsa-miR-125a-5p hsa-miR-3133 hsa-miR-340 hsa-miR-125b hsa-miR-186 hsa-miR-205* hsa-miR-3174
    SwitchGear 3'UTR luciferase reporter plasmidDDX42 3' UTR sequence
    Inhib. RNA
    Products:
        
    OriGene RNAi products in human, mouse, rat for DDX42
    Predesigned siRNA for gene silencing in human, mouse, rat DDX42

    Gene Editing
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    Clone
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    OriGene ORF clones in mouse, rat for DDX42
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): DDX42 (NM_203499)
    Sino Biological Human cDNA Clone for DDX42
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for DDX42
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX42

    Cell Line
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    GenScript Custom overexpressing Cell Line Services for DDX42
    Browse ESI BIO Cell Lines and PureStem Progenitors for DDX42 
    In Situ Assay
    Products:
       

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX42


    (According to UniProtKB, COMPARTMENTS Subcellular localization database, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene.)
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    Subcellular locations from UniProtKB/Swiss-Prot
    DDX42_HUMAN, Q86XP3: Cytoplasm. Nucleus speckle. Nucleus, Cajal body. Note=Isoform 2 is present in Cajal bodies
    (CBs) and nuclear speckles
    Subcellular locations from COMPARTMENTS: 

    CompartmentConfidence
    nucleus5
    cytosol1

    Gene Ontology (GO): 5 cellular component terms:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0005634nucleus IDA--
    GO:0005730NOT nucleolus IDA--
    GO:0005737cytoplasm IDA--
    GO:0015030Cajal body IEA--
    GO:0016607nuclear speck IEA--

    DDX42 for ontologies           About GeneDecksing


    (SuperPaths according to PathCards, Pathways according to R&D Systems, Cell Signaling Technology, KEGG, PharmGKB, BioSystems, Sino Biological, Reactome, Tocris Bioscience, GeneGo (Thomson Reuters), QIAGEN, and/or UniProtKB, Sets of similar genes according to GeneDecks, Interaction Networks according to QIAGEN, and/or STRING, Interactions according to 1UniProtKB, 2MINT, 3I2D, and/or 4STRING, with links to IntAct and Ensembl, Ontologies according to Gene Ontology Consortium 01 Apr 2014 via Entrez Gene).
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    SuperPaths for DDX42 About    
    See pathways by source

    SuperPathContained pathways About
    1Spliceosome
    Spliceosome

    Pathways by source                                                                                                                                                                 See SuperPaths
    Show all pathways




    1 Kegg Pathway  (Kegg details for DDX42):
        Spliceosome


    DDX42 for pathways           About GeneDecksing

        Custom Pathway & Disease-focused RT2 Profiler PCR Arrays for DDX42
    Interactions:

        Search GeneGlobe Interaction Network for DDX42

    STRING Interaction Network Preview (showing 5 interactants - click image to see 25)

    Selected Interacting proteins for DDX42 (Q86XP32, 3 ENSP000003523084) via UniProtKB, MINT, STRING, and/or I2D (see all 800)
    InteractantInteraction Details
    GeneCardExternal ID(s)
    SF3A2Q154282, 3, ENSP000002214944MINT-5205620 MINT-7947479 I2D: score=2 STRING: ENSP00000221494
    RUVBL2Q9Y2302, 3, ENSP000002214134MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000221413
    SF3B1O755332, 3, ENSP000003353214MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000335321
    RECQL5O947622, 3MINT-63238 I2D: score=5 
    RUVBL1Q9Y2652, 3, ENSP000003182974MINT-7945693 MINT-7947479 I2D: score=1 STRING: ENSP00000318297
    About this table

    Gene Ontology (GO): 1 biological process term:    About this table

    GO IDQualified GO termEvidencePubMed IDs
    GO:0008104protein localization IDA19377511

    DDX42 for ontologies           About GeneDecksing



    (Chemical Compounds according to UniProtKB, Enzo Life Sciences, EMD Millipore, Tocris Bioscience, ApexBio, HMDB, BitterDB, and/or Novoseek, Ligands according to IUPHAR, and Drugs according to DrugBank, Enzo Life Sciences, and/or PharmGKB)
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    Browse Small Molecules at EMD Millipore
       Browse drugs & compounds from Enzo Life Sciences
      Browse compounds at ApexBio 

    Browse Tocris compounds for DDX42



    (Secondary structures according to fRNAdb,
    GenBank/EMBL/DDBJ Accessions according to
    Unigene (Build 236 Homo sapiens; Apr 25 2013) or GenBank,
    RefSeq according to Entrez Gene,
    DOTS (version 10), and/or AceView, transcript ids from Ensembl with links to UCSC,
    Conferences by KenesGroup, exon structure from GeneLoc, alternative splicing isoforms according to ASD and/or ECgene,
    siRNAs from OriGene, QIAGEN, shRNA from OriGene, microRNA from QIAGEN, SwitchGear Genomics,
    Tagged/untagged cDNA clones from OriGene, GenScript, DNA2.0, Vector BioLabs, Primers from OriGene, and/or QIAGEN )
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    REFSEQ mRNAs for DDX42 gene (2 alternative transcripts): 
    NM_007372.3  NM_203499.2  

    Selected Ensembl transcripts including schematic representations, and UCSC links where relevant (see all 19):
    ENST00000581135 ENST00000578681(uc002jbu.3) ENST00000583590(uc002jbv.3 uc010wps.2)
    ENST00000359353(uc002jbw.1) ENST00000580108 ENST00000578137 ENST00000584261
    ENST00000577940 ENST00000579511 ENST00000577978 ENST00000584010(uc002jbx.3)
    ENST00000581477 ENST00000578593(uc002jby.3) ENST00000584951 ENST00000579539
    ENST00000582985 ENST00000581767 ENST00000389924
    miRNA
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    Block miRNA regulation of human, mouse, rat DDX42 using miScript Target Protectors
    Selected qRT-PCR Assays for microRNAs that regulate DDX42 (see all 19):
    hsa-miR-549 hsa-miR-125a-5p hsa-miR-3133 hsa-miR-340 hsa-miR-125b hsa-miR-186 hsa-miR-205* hsa-miR-3174
    SwitchGear 3'UTR luciferase reporter plasmidDDX42 3' UTR sequence
    Inhib. RNA
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    Predesigned siRNA for gene silencing in human, mouse, rat DDX42
    Clone
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    OriGene clones in human, mouse for DDX42 (see all 13)
    OriGene ORF clones in mouse, rat for DDX42
    OriGene custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
    GenScript: all cDNA clones in your preferred vector (see all 2): DDX42 (NM_203499)
    DNA2.0 Custom Codon Optimized Gene Synthesis Service for DDX42
    Vector BioLabs ready-to-use adenovirus/AAV for human, mouse, rat DDX42
    Primer
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    OriGene qSTAR qPCR primer pairs in human, mouse for DDX42
    Pre-validated RT2 qPCR Primer Assay in human, mouse, rat DDX42
      QuantiTect SYBR Green Assays in human, mouse, rat DDX42
      QuantiFast Probe-based Assays in human, mouse, rat DDX42

    Selected AceView cDNA sequences (see all 300):

    CB215329 AW009662 BQ679613 AF147429 CD516379 BM743670 AW513354 BM550220 
    CB128477 AB036090 CK300795 BU185874 BM564503 AW502957 AI678965 AI149108 
    BQ232108 BE901178 BQ213215 CA446920 BM462117 CF143527 AK096751 BQ437381 

    GeneLoc Exon Structure

    Selected Alternative Splicing Database (ASD) splice patterns (SP) for DDX42 (see all 12)    About this scheme

    ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10a · 10b ^ 11a · 11b ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18a · 18b ^
    SP1:                                                                                -                             -                 -     -                     
    SP2:                                                                                -                             -                 -     -                     
    SP3:                                                                                                              -                 -     -                     
    SP4:                                            -     -                                                                                                         
    SP5:                                            -           -                                                                                                   

    ExUns: 19 ^ 20a · 20b ^ 21a · 21b ^ 22a · 22b · 22c · 22d · 22e
    SP1:              -     -                                       
    SP2:              -     -                                       
    SP3:              -     -                                       
    SP4:                                                            
    SP5:                                                            


    ECgene alternative splicing isoforms for DDX42

    (RNA expression data according to H-InvDB, NONCODE, miRBase, and RNAdb, Expression images according to data from BioGPS, Illumina Human BodyMap, and CGAP SAGE, Sets of similar genes according to GeneDecks, in vivo and in vitro expression data from LifeMap Discovery™, Protein expression images according to data from SPIRE 1MOPED, 2PaxDb, and 3MaxQB, plus additional links to SOURCE, and/or BioGPS, and/or UniProtKB,
    PCR Arrays from QIAGEN, Primers from OriGene, and/or QIAGEN, In Situ Hybridization Assays from Advanced Cell Diagnostics)
    About This Section

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    DDX42 expression in normal human tissues (normalized intensities)
    See probesets specificity/sensitivity at GeneAnnot
    About this imageBioGPS <intensity>2/3
    CGAP TAG: TAGGAAACAC
    DDX42 Expression
    About this image


    DDX42 expression in embryonic tissues and stem cells    About this table
    Data from LifeMap, the Embryonic Development and Stem Cells Database
     
     Eye (Sensory Organs)
             Retina
    DDX42 Protein expression data from MOPED1, PaxDb2 and MaxQB3    About this image

    DDX42 Protein Expression

    UniProtKB/Swiss-Prot: DDX42_HUMAN, Q86XP3
    Tissue specificity: Expressed in several cell lines (at protein level). Expressed in liver, lung, tonsil, thymus,
    muscle and pancreatic islets

        Custom PCR Arrays for DDX42
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    In Situ
    Assay Products:
     

     
    Advanced Cell Diagnostics RNAscope RNA in situ hybridization assays for DDX42

    (Orthologs according to 1,2HomoloGene (2older version, for species not in 1newer version), 3euGenes, 4SGD , 5MGI Mar 06 2013, with possible further links to Flybase and/or WormBase, and/or 6Ensembl pan taxonomic compara , Gene Trees according to Ensembl and TreeFam)
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    This gene was present in the common ancestor of eukaryotes.

    Orthologs for DDX42 gene from Selected species (see all 19)    About this table
    Organism Taxonomic
    classification
    Gene Description Human
    Similarity
    Orthology
    Type
    Details
    mouse
    (Mus musculus)
    Mammalia Ddx421 , 5 DEAD (Asp-Glu-Ala-Asp) box polypeptide 421, 5 90.77(n)1
    96.44(a)1
      11 (68.89 cM)5
    720471  NM_028074.41  NP_082350.31 
     1062169265 
    chicken
    (Gallus gallus)
    Aves DDX421 DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 77.54(n)
    88.98(a)
      419959  NM_001030926.1  NP_001026097.1 
    lizard
    (Anolis carolinensis)
    Reptilia DDX426
    DEAD (Asp-Glu-Ala-Asp) box helicase 42
    85(a)
    1 ↔ 1
    6(78561336-78584418)
    African clawed frog
    (Xenopus laevis)
    Amphibia BC043977.12   -- 76.19(n)    BC043977.1 
    zebrafish
    (Danio rerio)
    Actinopterygii ddx421 DEAD (Asp-Glu-Ala-Asp) box polypeptide 42 69.36(n)
    75.96(a)
      503932  NM_001037805.2  NP_001032894.2 
    fruit fly
    (Drosophila melanogaster)
    Insecta CG64181 CG6418 59.15(n)
    58.06(a)
      39218  NM_140156.3  NP_648413.1 
    worm
    (Caenorhabditis elegans)
    Secernentea C46F11.41 C46F11.4 58.18(n)
    57.39(a)
      175469  NM_065342.4  NP_497743.1 
    baker's yeast
    (Saccharomyces cerevisiae)
    Saccharomycetes DBP26
    Essential ATP-dependent RNA helicase of the DEAD-b...
    37(a)
    1 → many
    XIV(413639-416281) YNL112W
    thale cress
    (Arabidopsis thaliana)
    eudicotyledons AT2G473301 AT2G47330 56.5(n)
    53.67(a)
      819346  NM_130301.4  NP_566099.1 
    rice
    (Oryza sativa)
    Liliopsida Os03g03085001 Os03g0308500 54.06(n)
    50.67(a)
      4332617  NM_001056439.1  NP_001049904.1 


    ENSEMBL Gene Tree for DDX42 (if available)
    TreeFam Gene Tree for DDX42 (if available)

    (Paralogs according to 1HomoloGene,
    2Ensembl, and 3SIMAP, Pseudogenes according to 4Pseudogene.org Build 68)
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    Paralogs for DDX42 gene
    DDX462  DDX52  DDX172  DDX432  DDX532  
    17 SIMAP similar genes for DDX42 using alignment to 5 protein entries:     DDX42_HUMAN (see all proteins):
    DDX46    DDX47    DDX53    DDX54    DDX3X    DDX5
    EIF4A2    EIF4A1    DDX17    DDX43    DDX49    EIF4A3
    DDX3Y    DDX39B    DDX52    DDX39A    DDX41

    DDX42 for paralogs           About GeneDecksing



    (SNPs/Variants according to the 1NCBI SNP Database, 2Ensembl, 3PupaSUITE, 4UniProtKB, and DNA2.0, Linkage Disequilibrium by HapMap, Structural Variations(CNVs/InDels/Inversions) from the Database of Genomic Variants, Mutations from the Human Gene Mutation Database (HGMD), the Human Cytochrome P450 Allele Nomenclature Database, and the Locus Specific Mutation Databases (LSDB), Blood group antigen gene mutations by BGMUT, Resequencing Primers, Cancer Mutation PCR Arrays and Assays, and Copy Number PCR Arrays from QIAGEN)
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    Selected SNPs for DDX42 (see all 983)    About this table    
    Genomic DataTranscription Related DataAllele Frequencies
    SNP IDValidClinical
    significance
    Chr 17 posSequence#AA
    Chg
    TypeMore#Allele
    freq
    PopTotal
    sample
    More
    ----------
    rs573795081,2
    C--61853126(+) AAAGCC/TTTTTA 2 -- int12Minor allele frequency- T:0.05WA 120
    rs1427996061,2
    --61853194(+) TATATC/TGTAAC 2 -- int10--------
    rs604240911,2
    C,F--61853195(+) ATATTG/TTAACA 2 -- int12Minor allele frequency- T:0.06WA 120
    rs1446429081,2
    --61853208(+) TTAATA/GTAAGA 2 -- int10--------
    rs1831894951,2
    --61853257(+) TAGTCA/GTATAA 2 -- int10--------
    rs1484754731,2
    --61853260(+) TCATAC/TAATCA 2 -- int10--------
    rs1878061531,2
    --61853266(+) AATCAG/TCTCTT 2 -- int10--------
    rs1926241171,2
    C--61853282(+) CTTTAA/CGCTGA 2 -- int10--------
    rs1856113031,2
    --61853295(+) GGAGAA/GGGGAT 2 -- int10--------
    rs116516931,2
    C,F,H--61853326(+) CTAGCA/GTTTAC 2 -- int18Minor allele frequency- G:0.39WA NA CSA EA 369

    HapMap Linkage Disequilibrium report for DDX42 (61850963 - 61896677 bp)

    Structural Variations
         Database of Genomic Variants (DGV) 5 variations for DDX42:    About this table    
    Variant IDTypeSubtypePubMed ID
    esv2658528CNV Deletion23128226
    esv2716097CNV Deletion23290073
    nsv833510CNV Loss17160897
    nsv510720CNV Loss20534489
    nsv517272CNV Gain+Loss19592680

    Site Specific Mutation Identification with PCR Assays
    SeqTarget long-range PCR primers for resequencing DDX42
    DNA2.0 Custom Variant and Variant Library Synthesis for DDX42

    (in which this Gene is Involved, According to MalaCards, OMIM, UniProtKB, the University of Copenhagen DISEASES database, Conferences by KenesGroup, Genatlas, GeneTests, GAD, HuGE Navigator, and/or TGDB.)
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    OMIM gene information: 613369    OMIM disorders: --

    6 diseases for DDX42:    
    About MalaCards
    japanese encephalitis    encephalitis    tonsillitis    fanconi's anemia
    pancreatitis    malaria


    DDX42 for disorders           About GeneDecksing


    Export disorders for DDX42 gene to outside databases

    (in PubMed. Associations of this gene to articles via 1Entrez Gene, 2UniProtKB/Swiss-Prot, 3HGNC, 4GAD, 5PharmGKB, 6HMDB, 7DrugBank, 8UniProtKB/TrEMBL, 9 Novoseek, and/or 10fRNAdb)
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    PubMed articles for DDX42 gene, integrated from 10 sources (see all 38):
    (articles sorted by number of sources associating them with DDX42)
        Utopia: connect your pdf to the dynamic
    world of online information

    1. Identification of a novel human member of the DEAD box protein family. (PubMed id 10727850)1, 2, 3, 9 Suk K.... Lee M.-S. (Biochim. Biophys. Acta 2000)
    2. Ddx42p -- a human DEAD box protein with RNA chaperone activities. (PubMed id 16397294)1, 2, 3 Uhlmann-Schiffler H.... Stahl H. (Nucleic Acids Res. 2006)
    3. Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein. (PubMed id 12234937)1, 2, 9 Will C.L.... Luehrmann R. (EMBO J. 2002)
    4. The DEAD box protein Ddx42p modulates the function of ASPP2, a stimulator of apoptosis. (PubMed id 19377511)1, 2 Uhlmann-Schiffler H.... Stahl H. (Oncogene 2009)
    5. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PubMed id 17081983)1, 2 Olsen J.V....Mann M. (Cell 2006)
    6. Complete sequencing and characterization of 21,243 full-length human cDNAs. (PubMed id 14702039)1, 2 Ota T.... Sugano S. (Nat. Genet. 2004)
    7. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PubMed id 15489334)1, 2 Gerhard D.S.... Malek J. (Genome Res. 2004)
    8. The F-box protein FBXO25 promotes the proteasome-dependent degradation of ELK-1 protein. (PubMed id 23940030)1 Teixeira F.R....Gomes M.D. (J. Biol. Chem. 2013)
    9. Pathway Analysis of ChIP-Seq-Based NRF1 Target Genes Suggests a Logical Hypothesis of their Involvement in the Pathogenesis of Neurodegenerative Diseases. (PubMed id 24250222)1 Satoh J....Yamamoto Y. (Gene Regul Syst Bio 2013)
    10. A census of human soluble protein complexes. (PubMed id 22939629)1 Havugimana P.C....Emili A. (Cell 2012)

    (in PubMed, OMIM, and NCBI Bookshelf)
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     ANDOR
    Aliases
    Free Text  

      Query String
    PubMed
    OMIM
    NCBI Bookshelf
      (Note: In FireFox, select the above section and copy using Ctrl-C)

    (According to Entrez Gene, HGNC, AceView, euGenes, Ensembl, miRBase, ECgene, Kegg, and/or H-InvDB)
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    Entrez Gene: 11325 HGNC: 18676 AceView: DDX42 Ensembl:ENSG00000198231 euGenes: HUgn11325
    ECgene: DDX42 Kegg: 11325 H-InvDB: DDX42

    (According to HUGE)
    About This Section

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      --

    (According to PharmGKB, ATLAS, HORDE, IMGT, LEIDEN, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL, and/or others, e.g. Wikipedia and GeneReviews, via UniProtKB/Swiss-Prot)
    About This Section

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    NameDescription
    PharmGKB entry for DDX42 Pharmacogenomics, SNPs, Pathways

    (Patent information from GeneIP,
    Licensable technologies from WIS Yeda, Salk, Tufts,
    IP news from LifeMap Sciences, Inc.)
    About This Section

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    Patent Information for DDX42 gene:
    Search GeneIP for patents involving DDX42

    GeneCards and IP:
    Japan Patent Office Licenses GeneCards     European Patent Office Licenses GeneCards     Improving the IP Search



    (Antibodies, recombinant proteins, and assays from EMD Millipore, R&D Systems, OriGene, QIAGEN, GenScript, Cell Signaling Technology, Novus Biologicals, Sino Biological, Enzo Life Sciences, Abcam, ProSpec, Cloud-Clone Corp., Thermo Fisher Scientific, LSBio, Gene Editing from DNA2.0. Clones from OriGene, GenScript, Sino Biological, DNA2.0, SwitchGear Genomics, Vector BioLabs, Cell lines from GenScript, and ESI BIO, PCR Arrays from QIAGEN, Drugs and/or compounds from EMD Millipore, Tocris Bioscience, Enzo Life Sciences, and/or ApexBio, In Situ Hybridization Assays from
    Advanced Cell Diagnostics, Animal models from inGenious Targeting Laboratory, genOway)
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