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

Gene ID: 13209, updated on 19-Mar-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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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

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