Ddx21 DExD box helicase 21 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Ddx21provided by MGI
Official Full Name: DExD box helicase 21provided by MGI
Primary source: MGI:MGI:1860494
See related: Ensembl:ENSMUSG00000020075 AllianceGenome:MGI:1860494
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: D10Wsu42e; D10Ertd645e
Summary: Enables double-stranded RNA binding activity and identical protein binding activity. Involved in positive regulation of canonical NF-kappaB signal transduction and positive regulation of myeloid dendritic cell cytokine production. Acts upstream of or within response to exogenous dsRNA and response to virus. Located in cytosol. Is expressed in several structures, including 1st branchial arch; cerebral cortex; early conceptus; genitourinary system; and limb. Orthologous to human DDX21 (DExD-box helicase 21). [provided by Alliance of Genome Resources, Oct 2024]
Expression: Ubiquitous expression in CNS E11.5 (RPKM 23.3), liver E14 (RPKM 22.6) and 25 other tissues See more
Orthologs: human all
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Genomic context

Location:: 10 B4; 10 32.43 cM

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	10	NC_000076.7 (62416026..62438077, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	10	NC_000076.6 (62580247..62602298, complement)

Chromosome 10 - NC_000076.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Mouse ENCODE transcriptome data 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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification.
Title: DDX21 is a p38-MAPK-sensitive nucleolar protein necessary for mouse preimplantation embryo development and cell-fate specification.
TLR4/NF-kappaB-responsive microRNAs and their potential target genes: a mouse model of skeletal muscle ischemia-reperfusion injury.
Title: TLR4/NF-κB-responsive microRNAs and their potential target genes: a mouse model of skeletal muscle ischemia-reperfusion injury.
a previously unknown function of the DDX21-TRIF-S100A9-TLR4-MyD88 signaling network in regulating inflammation during infection.
Title: DAMP molecule S100A9 acts as a molecular pattern to enhance inflammation during influenza A virus infection: role of DDX21-TRIF-TLR4-MyD88 pathway.
DDX1-DDX21-DHX36 complex represents a dsRNA sensor that uses the TRIF pathway to activate type I IFN responses in the cytosol of myeloid dendritic cells
Title: DDX1, DDX21, and DHX36 helicases form a complex with the adaptor molecule TRIF to sense dsRNA in dendritic cells.
in addition to its transcriptional effects, c-Jun regulates rRNA processing and nucleolar compartmentalization of the rRNA processing protein DDX21
Title: c-Jun supports ribosomal RNA processing and nucleolar localization of RNA helicase DDX21.
RNA helicase II/Gualpha silencing inhibits mammalian ribosomal RNA production
Title: Silencing of RNA helicase II/Gualpha inhibits mammalian ribosomal RNA production.

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Variation

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Alleles

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

Chemically induced (ENU) (1)
Endonuclease-mediated (6)
Targeted (1)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RH136022 (e-PCR)
- UniSTS:210018

D10Ertd645e (e-PCR), detects polymorphism
- UniSTS:167026

RH126535 (e-PCR)
- UniSTS:141529

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables 7SK snRNA binding	ISO Inferred from Sequence Orthology more info
enables 7SK snRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info	PubMed
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables identical protein binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables miRNA binding	ISO Inferred from Sequence Orthology more info
enables miRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables rRNA binding	ISO Inferred from Sequence Orthology more info
enables rRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables snoRNA binding	ISO Inferred from Sequence Orthology more info
enables snoRNA binding	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in R-loop processing	ISO Inferred from Sequence Orthology more info
involved_in R-loop processing	ISS Inferred from Sequence or Structural Similarity more info
involved_in chromatin remodeling	NAS Non-traceable Author Statement more info	PubMed
involved_in defense response to virus	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of canonical NF-kappaB signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of myeloid dendritic cell cytokine production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase I	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	NAS Non-traceable Author Statement more info	PubMed
involved_in positive regulation of transcription by RNA polymerase III	ISO Inferred from Sequence Orthology more info
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to exogenous dsRNA	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to virus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
involved_in transcription by RNA polymerase II	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
part_of B-WICH complex	ISO Inferred from Sequence Orthology more info
located_in chromosome	ISO Inferred from Sequence Orthology more info
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in mitochondrion	NAS Non-traceable Author Statement more info	PubMed
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleolus	ISS Inferred from Sequence or Structural Similarity more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info	PubMed

General protein information

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Preferred Names: nucleolar RNA helicase 2

Names: DEAD (Asp-Glu-Ala-Asp) box polypeptide 21; DEAD box protein 21; DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 21 (RNA helicase II/Gu); RH II/Gu; RH-II/Gualpha; gu-alpha; nucleolar RNA helicase Gu; nucleolar RNA helicase II

NP_062426.2

EC 3.6.4.13

XP_030101041.1

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_019553.2 → NP_062426.2 nucleolar RNA helicase 2

See identical proteins and their annotated locations for NP_062426.2

Status: VALIDATED

Source sequence(s)

BC059237, BC060220, CF182162

Consensus CDS

CCDS23891.1

UniProtKB/Swiss-Prot

Q3TVJ3, Q9JIK5, Q9WV45

UniProtKB/TrEMBL

Q3ULC7, Q6PCP0

Related

ENSMUSP00000042691.8, ENSMUST00000045866.9

Conserved Domains (5) summary

PRK01297
Location:191 → 633

PRK01297; ATP-dependent RNA helicase RhlB; Provisional

cd00079
Location:501 → 610

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 ...

cd00268
Location:260 → 467

DEADc; DEAD-box helicases. A diverse family of proteins involved in ATP-dependent RNA unwinding, needed in a variety of cellular processes including splicing, ribosome biogenesis and RNA degradation. The name derives from the sequence of the Walker B motif ...

cd12936
Location:689 → 781

GUCT_RHII_Gualpha_beta; RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins

cl17173
Location:794 → 840

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...

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

NC_000076.7 Reference GRCm39 C57BL/6J

Range

62416026..62438077 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030245181.1 → XP_030101041.1 nucleolar RNA helicase 2 isoform X1

Conserved Domains (3) summary

cd12936
Location:234 → 326

GUCT_RHII_Gualpha_beta; RNA-binding GUCT domain found in vertebrate RNA helicase II/Gualpha (RH-II/Gualpha), RNA helicase II/Gubeta (RH-II/Gubeta) and similar proteins

cd18787
Location:29 → 158

SF2_C_DEAD; C-terminal helicase domain of the DEAD box helicases

cl17173
Location:339 → 385

AdoMet_MTases; S-adenosylmethionine-dependent methyltransferases (SAM or AdoMet-MTase), class I; AdoMet-MTases are enzymes that use S-adenosyl-L-methionine (SAM or AdoMet) as a substrate for methyltransfer, creating the product S-adenosyl-L-homocysteine (AdoHcy). ...