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

Gene ID: 72047, updated on 5-Mar-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 protein localization and regulation of apoptotic process. Predicted to be located in cytosol and nuclear speck. Predicted to be active in nucleus. Orthologous to human DDX42 (DEAD-box helicase 42). [provided by Alliance of Genome Resources, Apr 2022]
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
  • 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 (32) 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)
  • Gene trapped (1) 
  • Targeted (2) 
  • Endonuclease-mediated (1) 

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 RNA binding ISO
Inferred from Sequence Orthology
more info
  
enables RNA helicase activity ISO
Inferred from Sequence Orthology
more info
  
enables helicase activity IEA
Inferred from Electronic Annotation
more info
  
enables hydrolase activity IEA
Inferred from Electronic Annotation
more info
  
enables nucleic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables nucleotide binding IEA
Inferred from Electronic Annotation
more info
  
Process Evidence Code Pubs
involved_in U2-type prespliceosome assembly ISO
Inferred from Sequence Orthology
more info
  
involved_in protein localization ISO
Inferred from Sequence Orthology
more info
  
involved_in regulation of apoptotic process ISO
Inferred from Sequence Orthology
more info
  
Component Evidence Code Pubs
part_of U2-type prespliceosome ISO
Inferred from Sequence Orthology
more info
  
located_in cytoplasm ISO
Inferred from Sequence Orthology
more info
  
located_in cytosol ISO
Inferred from Sequence Orthology
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
  

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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