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

    Gene ID: 11325, updated on 9-Dec-2024

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    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

    Expression

    • Project title: 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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 ATP-dependent H2AZ histone chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables ATP-dependent H3-H4 histone complex chaperone activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables DNA clamp loader 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 chromatin extrusion motor activity IEA
    Inferred from Electronic Annotation
    more info
     
    enables cohesin loader activity IEA
    Inferred from Electronic Annotation
    more info
     
    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 chromatin looping IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chromatin remodeling IEA
    Inferred from Electronic Annotation
    more info
     
    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

    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)

    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_007372.3NP_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:254688
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd00079
      Location:470601
      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:255459
      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_203499.3NP_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:254688
      PRK10590; ATP-dependent RNA helicase RhlE; Provisional
      cd00079
      Location:470601
      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:255459
      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_047435282.1XP_047291238.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
    2. XM_047435281.1XP_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_047435283.1XP_047291239.1  ATP-dependent RNA helicase DDX42 isoform X2

      UniProtKB/TrEMBL
      B3KX23

    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_054314931.1XP_054170906.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
    2. XM_054314930.1XP_054170905.1  ATP-dependent RNA helicase DDX42 isoform X1

      UniProtKB/Swiss-Prot
      A6NML1, A8KA43, O75619, Q68G51, Q86XP3, Q96BK1, Q96HR7, Q9Y3V8
    3. XM_054314932.1XP_054170907.1  ATP-dependent RNA helicase DDX42 isoform X2

      UniProtKB/TrEMBL
      B3KX23