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

Gene ID: 11325, updated on 3-Apr-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
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Genomic context

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Location:
17q23.3
Exon count:
21
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (63773800..63819317)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (64644531..64690152)
105.20220307 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, matrix associated, actin dependent regulator of chromatin, subfamily d, member 2

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
  • 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. 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
  3. Ddx42p--a human DEAD box protein with RNA chaperone activities. Uhlmann-Schiffler H, et al. Nucleic Acids Res, 2006. PMID 16397294, Free PMC Article
  4. Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly. Yang F, et al. Nat Commun, 2023 Feb 17. PMID 36797247, Free PMC Article
  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 (94) 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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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_2023_10

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

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