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    Ddx42 DEAD box helicase 42 [ Mus musculus (house mouse) ]

    Gene ID: 72047, updated on 28-Oct-2024

    Summary

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    Official Symbol
    Ddx42provided by MGI
    Official Full Name
    DEAD box helicase 42provided by MGI
    Primary source
    MGI:MGI:1919297
    See related
    Ensembl:ENSMUSG00000020705 AllianceGenome:MGI:1919297
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Mus musculus
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
    Also known as
    RHELP; RNAHP; SF3b125; 1810047H21Rik; B430002H05Rik
    Summary
    Predicted to enable RNA binding activity and RNA helicase activity. Predicted to be involved in U2-type prespliceosome assembly; protein localization; and regulation of apoptotic process. Predicted to be located in cytosol and nuclear speck. Predicted to be part of U2-type prespliceosome. Predicted to be active in nucleus. Orthologous to human DDX42 (DEAD-box helicase 42). [provided by Alliance of Genome Resources, Oct 2024]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 21.4), CNS E14 (RPKM 14.0) and 27 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ddx42 in Genome Data Viewer
    Location:
    11 E1; 11 68.89 cM
    Exon count:
    18
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 11 NC_000077.7 (106107715..106139966)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 11 NC_000077.6 (106216887..106249140)

    Chromosome 11 - NC_000077.7Genomic Context describing neighboring genes Neighboring gene STE20-related kinase adaptor alpha Neighboring gene STARR-positive B cell enhancer ABC_E7078 Neighboring gene STARR-positive B cell enhancer ABC_E739 Neighboring gene coiled-coil domain containing 47 Neighboring gene STARR-positive B cell enhancer ABC_E5285 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:106078089-106078198 Neighboring gene STARR-positive B cell enhancer ABC_E7080 Neighboring gene STARR-positive B cell enhancer ABC_E5286 Neighboring gene STARR-positive B cell enhancer ABC_E597 Neighboring gene FtsJ RNA 2'-O-methyltransferase 3 Neighboring gene protease (prosome, macropain) 26S subunit, ATPase 5 Neighboring gene predicted gene, 23645 Neighboring gene CapStarr-seq enhancer MGSCv37_chr11:106130475-106130662 Neighboring gene SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2 Neighboring gene STARR-positive B cell enhancer ABC_E598

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data Mouse ENCODE transcriptome data
    • Description: RNA profiling data sets generated by the Mouse ENCODE project.
    • BioProject: PRJNA66167
    • Publication: PMID 25409824
    • Analysis date: n/a

    Bibliography

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    Related articles in PubMed

    1. A survey of genes expressed in undifferentiated mouse embryonal carcinoma F9 cells: characterization of low-abundance mRNAs. Nishiguchi S, et al. J Biochem, 1994 Jul. PMID 7798170
    2. Placentation defects are highly prevalent in embryonic lethal mouse mutants. Perez-Garcia V, et al. Nature, 2018 Mar 22. PMID 29539633, Free PMC Article
    3. Phosphoproteomic analysis of the developing mouse brain. Ballif BA, et al. Mol Cell Proteomics, 2004 Nov. PMID 15345747
    4. A germline-specific class of small RNAs binds mammalian Piwi proteins. Girard A, et al. Nature, 2006 Jul 13. PMID 16751776
    5. Complementary proteomics strategies capture an ataxin-1 interactome in Neuro-2a cells. Zhang S, et al. Sci Data, 2018 Nov 20. PMID 30457570, Free PMC Article

    See all (34) citations in PubMed

    GeneRIFs: Gene References Into Functions

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)
    • Endonuclease-mediated (1) 
    • Gene trapped (1) 
    • Targeted (2) 

    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

    Gene Ontology Provided by MGI

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in U2-type prespliceosome assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in U2-type prespliceosome assembly ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in protein localization ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in protein localization ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in regulation of apoptotic process ISO
    Inferred from Sequence Orthology
    more info
    		  
    involved_in regulation of apoptotic process ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    Component Evidence Code Pubs
    part_of U2-type prespliceosome ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of U2-type prespliceosome ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nuclear speck IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in nuclear speck ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  

    General protein information

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    Preferred Names
    ATP-dependent RNA helicase DDX42
    Names
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 42
    DEAD box protein 42
    RNA helicase-related protein
    NP_001348569.1
    NP_001348571.1
    NP_001348572.1
    NP_001348573.1
    NP_082350.3
    XP_030102205.1
    XP_036012900.1

    NCBI Reference Sequences (RefSeq)

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    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_001361640.1 → NP_001348569.1  ATP-dependent RNA helicase DDX42 isoform b

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (b) is shorter at the N-terminus compared to isoform a.
      Source sequence(s)
      AL604045
      Conserved Domains (2) summary
      PTZ00110
      Location:30 → 489
      PTZ00110; helicase; Provisional
      cl11081
      Location:481 → 726
      dermokine

    2. NM_001361642.1 → NP_001348571.1  ATP-dependent RNA helicase DDX42 isoform c

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and coding sequence and lacks two alternate in-frame exons compared to variant 1. The resulting isoform (c) is shorter at the N-terminus and lacks an alternate internal segment compared to isoform a.
      Source sequence(s)
      AL604045
      Conserved Domains (1) summary
      COG0513
      Location:76 → 343
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

    3. NM_001361643.1 → NP_001348572.1  ATP-dependent RNA helicase DDX42 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AK134182, AL596331, AL604045
      Conserved Domains (2) summary
      PRK10590
      Location:9 → 414
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd17952
      Location:1 → 196
      DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42

    4. NM_001361644.1 → NP_001348573.1  ATP-dependent RNA helicase DDX42 isoform d

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence compared to variant 1. The resulting isoform (d) is shorter at the N-terminus compared to isoform a. Variants 4 and 5 both encode the same isoform (d).
      Source sequence(s)
      AL604045
      Conserved Domains (2) summary
      PRK10590
      Location:9 → 414
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd17952
      Location:1 → 196
      DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42

    5. NM_028074.4 → NP_082350.3  ATP-dependent RNA helicase DDX42 isoform a

      See identical proteins and their annotated locations for NP_082350.3

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (a).
      Source sequence(s)
      AI836088, AK007805, AK049311
      Consensus CDS
      CCDS48956.1
      UniProtKB/Swiss-Prot
      Q3TAN3, Q3TE60, Q810A7, Q8BWZ7, Q9D8Q2
      Related
      ENSMUSP00000021046.6, ENSMUST00000021046.6
      Conserved Domains (3) summary
      PRK10590
      Location:254 → 678
      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_000001635.27-RS_2024_02

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

    Reference GRCm39 C57BL/6J

    Genomic

    1. NC_000077.7 Reference GRCm39 C57BL/6J

      Range
      106107715..106139966
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_036157007.1 → XP_036012900.1  ATP-dependent RNA helicase DDX42 isoform X1

      Conserved Domains (2) summary
      PTZ00110
      Location:30 → 489
      PTZ00110; helicase; Provisional
      cl11081
      Location:481 → 726
      dermokine

    2. XM_030246345.2 → XP_030102205.1  ATP-dependent RNA helicase DDX42 isoform X2

      Conserved Domains (2) summary
      PRK10590
      Location:9 → 414
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd17952
      Location:1 → 196
      DEADc_DDX42; DEAD-box helicase domain of DEAD box protein 42
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q810A7.3 GenPept UniProtKB/Swiss-Prot:Q810A7

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