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    DDX42 DEAD-box helicase 42 [ Homo sapiens (human) ]

    Gene ID: 11325, updated on 2-Nov-2024

    Summary

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    Official Symbol
    DDX42provided by HGNC
    Official Full Name
    DEAD-box helicase 42provided by HGNC
    Primary source
    HGNC:HGNC:18676
    See related
    Ensembl:ENSG00000198231 MIM:613369; AllianceGenome:HGNC:18676
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    RHELP; RNAHP; SF3B8; DDX42P; SF3b125
    Summary
    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]
    Expression
    Ubiquitous expression in testis (RPKM 27.4), ovary (RPKM 25.5) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX42 in Genome Data Viewer
    Location:
    17q23.3
    Exon count:
    21
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63773800..63819317)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64644531..64690152)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (61851530..61896677)

    Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 9817 Neighboring gene STE20 related adaptor alpha Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:61817285-61817784 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8830 Neighboring gene coiled-coil domain containing 47 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:61850832-61851416 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8831 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr17:61897185-61898384 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr17:61904136-61905335 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12563 Neighboring gene Sharpr-MPRA regulatory region 8123 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 12564 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 8832 Neighboring gene proteasome 26S subunit, ATPase 5 Neighboring gene SWI/SNF related BAF chromatin remodeling complex subunit D2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. [The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses]. Bonaventure B, et al. Med Sci (Paris), 2023 Apr. PMID 37094262
    2. Ddx42p--a human DEAD box protein with RNA chaperone activities. Uhlmann-Schiffler H, et al. Nucleic Acids Res, 2006. PMID 16397294, Free PMC Article
    3. The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses. Bonaventure B, et al. EMBO Rep, 2022 Nov 7. PMID 36161446, Free PMC Article
    4. Identification of a novel human member of the DEAD box protein family. Suk K, et al. Biochim Biophys Acta, 2000 Apr 15. PMID 10727850
    5. Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42. Zhao B, et al. J Biochem, 2022 Jul 25. PMID 35652295

    See all (108) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. [The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses].
      Title: [The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses].
    2. Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
      Title: Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly.
    3. The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses.
      Title: The DEAD box RNA helicase DDX42 is an intrinsic inhibitor of positive-strand RNA viruses.
    4. Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42.
      Title: Cancer-associated mutations in SF3B1 disrupt the interaction between SF3B1 and DDX42.
    5. expression of N-terminal DDX42 is able to overcome Japanese encephalitis virus-induced antagonism of IFN responses and so may be important for Japanese encephalitis virus pathogenesis
      Title: Interferon antagonist function of Japanese encephalitis virus NS4A and its interaction with DEAD-box RNA helicase DDX42.
    6. characterization of protein associated with the human 17S U2 snRNP and one of its stable subunits, SF3b; may facilitate the assembly of the 17S U2 snRNP
      Title: Characterization of novel SF3b and 17S U2 snRNP proteins, including a human Prp5p homologue and an SF3b DEAD-box protein.
    7. Ddx42p represents the first example of a human DEAD box protein possessing RNA helicase, protein displacement and RNA annealing activities.
      Title: Ddx42p--a human DEAD box protein with RNA chaperone activities.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ39432, FLJ43179

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables ATP binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables ATP hydrolysis activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding HDA PubMed 
    enables RNA binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables RNA helicase activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in U2-type prespliceosome assembly IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in protein localization IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of apoptotic process IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in Cajal body IEA
    Inferred from Electronic Annotation
    more info
    		  
    part_of U2-type prespliceosome IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		  
    located_in membrane HDA PubMed 
    located_in nuclear speck IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DDX42
    Names
    DEAD (Asp-Glu-Ala-Asp) box helicase 42
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 42
    SF3b DEAD box protein
    splicing factor 3B-associated 125 kDa protein
    splicing factor 3b, subunit 8
    NP_031398.2
    NP_987095.1
    XP_047291237.1
    XP_047291238.1
    XP_047291239.1
    XP_054170905.1
    XP_054170906.1
    XP_054170907.1

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    mRNA and Protein(s)

    1. NM_007372.3 → NP_031398.2  ATP-dependent RNA helicase DDX42

      See identical proteins and their annotated locations for NP_031398.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC015651, BC015505, BC093081
      Consensus CDS
      CCDS32704.1
      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
      Related
      ENSP00000464050.1, ENST00000578681.5
      Conserved Domains (3) summary
      PRK10590
      Location:254 → 688
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd00079
      Location:470 → 601
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cd00268
      Location:255 → 459
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

    2. NM_203499.3 → NP_987095.1  ATP-dependent RNA helicase DDX42

      See identical proteins and their annotated locations for NP_987095.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AB036090, AC015651, BC015505, DA440475
      Consensus CDS
      CCDS32704.1
      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
      Related
      ENSP00000374574.2, ENST00000389924.7
      Conserved Domains (3) summary
      PRK10590
      Location:254 → 688
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd00079
      Location:470 → 601
      HELICc; Helicase superfamily c-terminal domain; associated with DEXDc-, DEAD-, and DEAH-box proteins, yeast initiation factor 4A, Ski2p, and Hepatitis C virus NS3 helicases; this domain is found in a wide variety of helicases and helicase related proteins; may ...
      cd00268
      Location:255 → 459
      DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

      Range
      63773800..63819317
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047435282.1 → XP_047291238.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8

    2. XM_047435281.1 → XP_047291237.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
      Related
      ENSP00000463561.1, ENST00000583590.5

    3. XM_047435283.1 → XP_047291239.1  ATP-dependent RNA helicase DDX42 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060941.1 Alternate T2T-CHM13v2.0

      Range
      64644531..64690152
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314931.1 → XP_054170906.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8

    2. XM_054314930.1 → XP_054170905.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8

    3. XM_054314932.1 → XP_054170907.1  ATP-dependent RNA helicase DDX42 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q86XP3.1 GenPept UniProtKB/Swiss-Prot:Q86XP3

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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