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    DDX56 DEAD-box helicase 56 [ Homo sapiens (human) ]

    Gene ID: 54606, updated on 3-Nov-2024

    Summary

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    Official Symbol
    DDX56provided by HGNC
    Official Full Name
    DEAD-box helicase 56provided by HGNC
    Primary source
    HGNC:HGNC:18193
    See related
    Ensembl:ENSG00000136271 MIM:608023; AllianceGenome:HGNC:18193
    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
    DDX21; DDX26; NOH61
    Summary
    This gene encodes a member of the DEAD box protein family. DEAD box proteins, characterized by the conserved motif Asp-Glu-Ala-Asp (DEAD), are putative RNA helicases. They 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. Based on their distribution patterns, some members of this family are believed to be involved in embryogenesis, spermatogenesis, and cellular growth and division. The protein encoded by this gene shows ATPase activity in the presence of polynucleotides and associates with nucleoplasmic 65S preribosomal particles. This gene may be involved in ribosome synthesis, most likely during assembly of the large 60S ribosomal subunit. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2012]
    Expression
    Ubiquitous expression in thyroid (RPKM 15.8), lymph node (RPKM 15.1) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See DDX56 in Genome Data Viewer
    Location:
    7p13
    Exon count:
    14
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44565804..44573908, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44725568..44733672, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (44605403..44613507, complement)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene ribosomal protein L36a pseudogene 27 Neighboring gene NPC1 like intracellular cholesterol transporter 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25941 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44579601-44580222 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44600956-44601850 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44605263-44605762 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25942 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18145 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18146 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25944 Neighboring gene transmembrane p24 trafficking protein 4 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25945 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18147 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:44646637-44647200 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25947 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18148 Neighboring gene oxoglutarate dehydrogenase Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25948 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25949 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44674956-44675111 Neighboring gene OGDH intron CAGE-defined high expression enhancer Neighboring gene ATAC-STARR-seq lymphoblastoid active region 25951 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:44679045-44679572 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44685039-44685539 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:44717745-44717958 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:44740093-44740593

    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 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 nucleolar helicase DDX56 redistributes to West Nile virus assembly sites. Reid CR, et al. Virology, 2017 Jan. PMID 27821284
    2. A novel helicase-type protein in the nucleolus: protein NOH61. Zirwes RF, et al. Mol Biol Cell, 2000 Apr. PMID 10749921, Free PMC Article
    3. Molecular characterization of DDX26, a human DEAD-box RNA helicase, located on chromosome 7p12. Camargo AA, et al. Braz J Med Biol Res, 2001 Oct. PMID 11593297
    4. The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles. Xu Z, et al. Virology, 2012 Nov 10. PMID 22925334, Free PMC Article
    5. DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma. Wu Q, et al. Mol Cancer, 2021 Aug 26. PMID 34446021, Free PMC Article

    See all (119) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DDX56 transcriptionally activates MIST1 to facilitate tumorigenesis of HCC through PTEN-AKT signaling.
      Title: DDX56 transcriptionally activates MIST1 to facilitate tumorigenesis of HCC through PTEN-AKT signaling.
    2. DEAD-box helicase 56 functions as an oncogene promote cell proliferation and invasion in gastric cancer via the FOXO1/p21 Cip1/c-Myc signaling pathway.
      Title: DEAD-box helicase 56 functions as an oncogene promote cell proliferation and invasion in gastric cancer via the FOXO1/p21 Cip1/c-Myc signaling pathway.
    3. DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma.
      Title: DDX56 modulates post-transcriptional Wnt signaling through miRNAs and is associated with early recurrence in squamous cell lung carcinoma.
    4. The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells.
      Title: The DEAD-box helicase DDX56 is a conserved stemness regulator in normal and cancer stem cells.
    5. DDX56 Binds to Chikungunya Virus RNA To Control Infection.
      Title: DDX56 Binds to Chikungunya Virus RNA To Control Infection.
    6. DDX56 inhibits type I interferon by disrupting assembly of IRF3-IPO5 to inhibit IRF3 nucleus import.
      Title: DDX56 inhibits type I interferon by disrupting assembly of IRF3-IPO5 to inhibit IRF3 nucleus import.
    7. Study identified DDX56 as a novel oncogene on chromosome 7p and a prognostic biomarker of colorectal cancer (CRC). DDX56 can induce oncogenic splicing abnormalities of the G2-M cell cycle checkpoint gene WEE1 which contributes to the inhibition of proliferation and cell cycle progression.
      Title: Oncogenic splicing abnormalities induced by DEAD-Box Helicase 56 amplification in colorectal cancer.
    8. West Nile virus infection results in relocalization of DDX56 from nucleoli to virus assembly sites on the endoplasmic reticululm (ER), an observation that is consistent with a role for DDX56 in WNV virion assembly.
      Title: The nucleolar helicase DDX56 redistributes to West Nile virus assembly sites.
    9. The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles.
      Title: The helicase activity of DDX56 is required for its role in assembly of infectious West Nile virus particles.
    10. Coimmunoprecipitation confirmed that capsid protein binds to human DDX56 in infected cells and that this interaction is required for assembly of infectious West Nile virus particles.
      Title: The capsid-binding nucleolar helicase DDX56 is important for infectivity of West Nile virus.
    Submit: New GeneRIF Correction See all GeneRIFs (11)

    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

    HIV-1 interactions

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    Protein interactions

    Protein Gene Interaction Pubs
    Rev rev DDX56 interacts with HIV-1 Rev and enhances the Rev function. DDX56 alters the subcellular localization of Rev from nucleolus to nucleus and co-localizes with Rev in the nucleus PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Potential readthrough

    Included gene: TMED4

    Homology

    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 helicase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables RNA stem-loop binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein sequestering activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in defense response to virus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    acts_upstream_of_negative_effect modulation by host of viral RNA genome replication IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of type I interferon production IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in positive regulation of neuron projection development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in rRNA processing IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in membrane HDA PubMed 
    is_active_in nucleolus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleolus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    probable ATP-dependent RNA helicase DDX56
    Names
    61-kd nucleolar helicase
    ATP-dependent 61 kDa nucleolar RNA helicase
    DEAD (Asp-Glu-Ala-Asp) box helicase 56
    DEAD (Asp-Glu-Ala-Asp) box polypeptide 56
    DEAD box protein 21
    DEAD box protein 56
    DEAD-box RNA helicase
    nucleolar helicase of 61 kDa
    putative nucleolar RNA helicase
    NP_001244118.1
    NP_061955.1

    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_001257189.2 → NP_001244118.1  probable ATP-dependent RNA helicase DDX56 isoform 2

      See identical proteins and their annotated locations for NP_001244118.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an alternate in-frame exon compared to variant 1. The resulting protein (isoform 2) is shorter compared to isoform 1.
      Source sequence(s)
      AC004938, AK315363, CA423604
      Consensus CDS
      CCDS59053.1
      UniProtKB/TrEMBL
      Q53HB9
      Related
      ENSP00000393488.1, ENST00000431640.5
      Conserved Domains (3) summary
      COG0513
      Location:9 → 473
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd00079
      Location:234 → 348
      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 ...
      cl21455
      Location:9 → 219
      P-loop_NTPase; P-loop containing Nucleoside Triphosphate Hydrolases

    2. NM_019082.4 → NP_061955.1  probable ATP-dependent RNA helicase DDX56 isoform 1

      See identical proteins and their annotated locations for NP_061955.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer protein (isoform 1).
      Source sequence(s)
      AK125595, BC001235
      Consensus CDS
      CCDS5492.1
      UniProtKB/Swiss-Prot
      A4D2K9, C9JV95, Q6IAE2, Q9H9I8, Q9NY93
      UniProtKB/TrEMBL
      Q53HB9
      Related
      ENSP00000258772.5, ENST00000258772.10
      Conserved Domains (2) summary
      COG0513
      Location:9 → 513
      SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]
      cd17961
      Location:14 → 220
      DEADc_DDX56; DEAD-box helicase domain of DEAD box protein 56

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      44565804..44573908 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      44725568..44733672 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9NY93.1 GenPept UniProtKB/Swiss-Prot:Q9NY93

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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