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

Gene ID: 54606, updated on 5-Mar-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
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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_2023_10 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (44565804..44573908, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (44725568..44733672, complement)
105.20220307 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
  • 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. 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
  2. The nucleolar helicase DDX56 redistributes to West Nile virus assembly sites. Reid CR, et al. Virology, 2017 Jan. PMID 27821284
  3. 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
  4. 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
  5. A novel helicase-type protein in the nucleolus: protein NOH61. Zirwes RF, et al. Mol Biol Cell, 2000 Apr. PMID 10749921, Free PMC Article

See all (103) 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_2023_10

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

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