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

Summary

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

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_000007.14 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
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.
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.
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.
DDX56 Binds to Chikungunya Virus RNA To Control Infection.
Title: DDX56 Binds to Chikungunya Virus RNA To Control Infection.
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.
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.
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.
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.
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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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)

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

D7S2312 (e-PCR)
- UniSTS:54359

D7S2173E (e-PCR)
- UniSTS:151160

RH80564 (e-PCR)
- UniSTS:86772

D7S2082E (e-PCR)
- UniSTS:20982

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 ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	HDA more info	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 chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
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 chromatin looping	IEA Inferred from Electronic Annotation more info
involved_in chromatin remodeling	IEA Inferred from Electronic Annotation more info
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 more info	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

EC 3.6.4.13

NP_061955.1

EC 3.6.4.13

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)

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
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