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    Ddx6 DEAD-box helicase 6 [ Mus musculus (house mouse) ]

    Gene ID: 13209, updated on 12-May-2024

    Summary

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    Official Symbol
    Ddx6provided by MGI
    Official Full Name
    DEAD-box helicase 6provided by MGI
    Primary source
    MGI:MGI:104976
    See related
    Ensembl:ENSMUSG00000032097 AllianceGenome:MGI:104976
    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
    p54; rck; HLR2; mRCK/P54; 1110001P04Rik; C430015D01Rik; E230023J21Rik
    Summary
    Predicted to enable mRNA binding activity and protein domain specific binding activity. Acts upstream of or within negative regulation of neuron differentiation and stem cell population maintenance. Located in P-body. Is expressed in several structures, including brain; early conceptus; neural tube; oocyte; and trunk somite. Orthologous to human DDX6 (DEAD-box helicase 6). [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Ubiquitous expression in CNS E11.5 (RPKM 19.5), CNS E14 (RPKM 15.0) and 28 other tissues See more
    Orthologs
    human all
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    Genomic context

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    See Ddx6 in Genome Data Viewer
    Location:
    9 A5.2; 9 24.84 cM
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_02 current GRCm39 (GCF_000001635.27) 9 NC_000075.7 (44514113..44552028)
    108.20200622 previous assembly GRCm38.p6 (GCF_000001635.26) 9 NC_000075.6 (44602983..44640731)

    Chromosome 9 - NC_000075.7Genomic Context describing neighboring genes Neighboring gene B cell CLL/lymphoma 9-like Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:44323517-44323626 Neighboring gene STARR-positive B cell enhancer ABC_E5066 Neighboring gene C-X-C motif chemokine receptor 5 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:44345968-44346210 Neighboring gene CapStarr-seq enhancer MGSCv37_chr9:44348167-44348368 Neighboring gene predicted gene, 50603 Neighboring gene STARR-positive B cell enhancer mm9_chr9:44379241-44379542 Neighboring gene STARR-seq mESC enhancer starr_23977 Neighboring gene STARR-positive B cell enhancer ABC_E6727 Neighboring gene STARR-seq mESC enhancer starr_23980 Neighboring gene STARR-positive B cell enhancer ABC_E10542 Neighboring gene predicted gene, 30671 Neighboring gene STARR-positive B cell enhancer ABC_E8287 Neighboring gene cDNA sequence BC049987 Neighboring gene NSA2 ribosome biogenesis homolog pseudogene

    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. RNA decay in processing bodies is indispensable for adipogenesis. Maeda R, et al. Cell Death Dis, 2021 Mar 17. PMID 33731683, Free PMC Article
    2. Expression of the DEAD-box/RNA helicase rck/p54 in mouse tissues: implications for heterogeneous protein expression. Akao Y, et al. J Histochem Cytochem, 2006 Aug. PMID 16618942
    3. Expression of rck/p54, a DEAD-box RNA helicase, in gametogenesis and early embryogenesis of mice. Matsumoto K, et al. Dev Dyn, 2005 Jul. PMID 15906376
    4. Cloning and expression of a murine cDNA homologous to the human RCK/P54, a lymphoma-linked chromosomal translocation junction gene on 11q23. Seto M, et al. Gene, 1995 Dec 12. PMID 8543178
    5. ES-mediated chimera analysis revealed requirement of DDX6 for NANOS2 localization and function in mouse germ cells. Shimada R, et al. Sci Rep, 2019 Jan 24. PMID 30679547, Free PMC Article

    See all (63) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing.
      Title: The RNA helicase DDX6 controls early mouse embryogenesis by repressing aberrant inhibition of BMP signaling through miRNA-mediated gene silencing.
    2. RNA decay in processing bodies is indispensable for adipogenesis.
      Title: RNA decay in processing bodies is indispensable for adipogenesis.
    3. DDX6-null germ cells exhibited both similar and distinct defects from those observed in NANOS2-null germ cells. These results demonstrate that NANOS2 function is carried out via both P-body-dependent and -independent mechanisms. RNA-seq analyses further supported the phenotypic differences between DDX6-null and NANOS2-null germ cells, and indicated distinct molecular cascades involved in NANOS2-mediated gene regulation.
      Title: ES-mediated chimera analysis revealed requirement of DDX6 for NANOS2 localization and function in mouse germ cells.
    4. DDX6 is required for maintaining the quiescent state of primordial follicles.
      Title: ELAVL2-directed RNA regulatory network drives the formation of quiescent primordial follicles.
    5. The Ddx6 knockout cells were phenotypically and molecularly similar to cells lacking all microRNAs (Dgcr8 knockout ESCs). These data show that the loss of DDX6 can separate the two canonical functions of microRNAs: translational repression and transcript destabilization
      Title: Decoupling the impact of microRNAs on translational repression versus RNA degradation in embryonic stem cells.
    6. Data show that RNA helicase DDX6 colocalizes with ubiquitin-protein ligase TRIM32 in neural stem cells and neurons and that it increases the activity of microRNA Let-7a.
      Title: The RNA helicase DDX6 regulates cell-fate specification in neural stem cells via miRNAs.
    7. RCK/ p54 might be a determinant of colorectal cancer proliferation by activating the canonical Wnt pathway
      Title: Knockdown of RCK/p54 expression by RNAi inhibits proliferation of human colorectal cancer cells in vitro and in vivo.
    8. rck/p54 may play an important role in gametogenesis and early embryogenesis in mammals
      Title: Expression of rck/p54, a DEAD-box RNA helicase, in gametogenesis and early embryogenesis of mice.
    9. rck/p54 protein was ubiquitously expressed in mouse tissues
      Title: Expression of the DEAD-box/RNA helicase rck/p54 in mouse tissues: implications for heterogeneous protein expression.
    Submit: New GeneRIF Correction

    Variation

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    Alleles

    Alleles of this type are documented at Mouse Genome Informatics  (MGI)

    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables hydrolase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables mRNA binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables nucleic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables nucleotide binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein domain specific binding ISO
    Inferred from Sequence Orthology
    more info
    		  
    Process Evidence Code Pubs
    involved_in P-body assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within P-body assembly ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    involved_in P-body assembly ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_positive_effect miRNA-mediated gene silencing by inhibition of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of_or_within negative regulation of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of translation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in negative regulation of translation ISO
    Inferred from Sequence Orthology
    more info
    		  
    acts_upstream_of neuron differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within stem cell population maintenance IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in stress granule assembly IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in viral RNA genome packaging ISO
    Inferred from Sequence Orthology
    more info
    		  
    Component Evidence Code Pubs
    is_active_in P-body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in P-body IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in P-body ISO
    Inferred from Sequence Orthology
    more info
    		 PubMed 
    part_of RISC complex ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in adherens junction ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in chromatoid body ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in concave side of sperm head ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytoplasmic ribonucleoprotein granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    is_active_in cytoplasmic stress granule IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasmic stress granule ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in cytosol ISO
    Inferred from Sequence Orthology
    more info
    		  
    part_of heterochromatin ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in nucleus ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in outer dense fiber ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in perinuclear region of cytoplasm ISO
    Inferred from Sequence Orthology
    more info
    		  
    located_in sperm annulus ISO
    Inferred from Sequence Orthology
    more info
    		  

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX6
    Names
    ATP-dependent RNA helicase p54
    D-E-A-D (aspartate-glutamate-alanine-aspartate) box polypeptide 6
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 6
    DEAD (aspartate-glutamate-alanine-aspartate) box polypeptide 6
    DEAD box protein 6
    DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 6
    oncogene RCK homolog
    NP_001104296.1
    NP_001344631.1
    NP_001344632.1
    NP_031867.1
    NP_851841.2
    XP_011240693.1
    XP_030099902.1

    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_001110826.1 → NP_001104296.1  probable ATP-dependent RNA helicase DDX6

      See identical proteins and their annotated locations for NP_001104296.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC151971, AK148483, CN528354
      Consensus CDS
      CCDS23116.1
      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Related
      ENSMUSP00000128421.2, ENSMUST00000170489.2
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    2. NM_001357702.1 → NP_001344631.1  probable ATP-dependent RNA helicase DDX6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC151971
      Consensus CDS
      CCDS23116.1
      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    3. NM_001357703.1 → NP_001344632.1  probable ATP-dependent RNA helicase DDX6

      Status: VALIDATED

      Description
      Transcript Variant: This variant (5) represents the longest transcript. All five variants encode the same protein.
      Source sequence(s)
      AC151971
      Consensus CDS
      CCDS23116.1
      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    4. NM_007841.4 → NP_031867.1  probable ATP-dependent RNA helicase DDX6

      See identical proteins and their annotated locations for NP_031867.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC151971, AK148483, CD353843
      Consensus CDS
      CCDS23116.1
      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    5. NM_181324.3 → NP_851841.2  probable ATP-dependent RNA helicase DDX6

      See identical proteins and their annotated locations for NP_851841.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 5. All five variants encode the same protein.
      Source sequence(s)
      AC151971, AK148483
      Consensus CDS
      CCDS23116.1
      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Related
      ENSMUSP00000149620.2, ENSMUST00000217034.2
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    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_000075.7 Reference GRCm39 C57BL/6J

      Range
      44514113..44552028
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011242391.4 → XP_011240693.1  probable ATP-dependent RNA helicase DDX6 isoform X1

      See identical proteins and their annotated locations for XP_011240693.1

      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6

    2. XM_030244042.2 → XP_030099902.1  probable ATP-dependent RNA helicase DDX6 isoform X1

      UniProtKB/Swiss-Prot
      O54979, P54823, Q3UFI3, Q8BW68
      Conserved Domains (2) summary
      cd18787
      Location:309 → 438
      SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases
      cd17940
      Location:98 → 299
      DEADc_DDX6; DEAD-box helicase domain of DEAD box protein 6
    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P54823.1 GenPept UniProtKB/Swiss-Prot:P54823

    Gene LinkOut

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