DDX21 DExD-box helicase 21 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DDX21provided by HGNC
Official Full Name: DExD-box helicase 21provided by HGNC
Primary source: HGNC:HGNC:2744
See related: Ensembl:ENSG00000165732 MIM:606357; AllianceGenome:HGNC:2744
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: RH; GUA; GURDB; II/Gu; RH II/Gu; RH-II/GU; gu-alpha; RH-II/GuA
Summary: 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. This gene encodes a DEAD box protein, which is an antigen recognized by autoimmune antibodies from a patient with watermelon stomach disease. This protein unwinds double-stranded RNA, folds single-stranded RNA, and may play important roles in ribosomal RNA biogenesis, RNA editing, RNA transport, and general transcription. [provided by RefSeq, Jul 2008]
Expression: Ubiquitous expression in bone marrow (RPKM 38.2), appendix (RPKM 33.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 10q22.1

Exon count:: 16

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	10	NC_000010.11 (68956170..68985068)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	10	NC_060934.1 (69825602..69854499)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	10	NC_000010.10 (70715926..70744824)

Chromosome 10 - NC_000010.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The RNA helicase DDX21 activates YAP to promote tumorigenesis and is transcriptionally upregulated by beta-catenin in colorectal cancer.
Title: The RNA helicase DDX21 activates YAP to promote tumorigenesis and is transcriptionally upregulated by β-catenin in colorectal cancer.
TRIP13 regulates progression of gastric cancer through stabilising the expression of DDX21.
Title: TRIP13 regulates progression of gastric cancer through stabilising the expression of DDX21.
U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis.
Title: U3 snoRNA inter-regulates with DDX21 in the perichromosomal region to control mitosis.
DDX21 mediates co-transcriptional RNA m[6]A modification to promote transcription termination and genome stability.
Title: DDX21 mediates co-transcriptional RNA m(6)A modification to promote transcription termination and genome stability.
Lnc-PLCB1 is stabilized by METTL14 induced m6A modification and inhibits Helicobacter pylori mediated gastric cancer by destabilizing DDX21.
Title: Lnc-PLCB1 is stabilized by METTL14 induced m6A modification and inhibits Helicobacter pylori mediated gastric cancer by destabilizing DDX21.
m[6]A-dependent upregulation of DDX21 by super-enhancer-driven IGF2BP2 and IGF2BP3 facilitates progression of acute myeloid leukaemia.
Title: m(6)A-dependent upregulation of DDX21 by super-enhancer-driven IGF2BP2 and IGF2BP3 facilitates progression of acute myeloid leukaemia.
Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid.
Title: Joint effect of RRP9 and DDX21 on development of colorectal cancer and keloid.
RRP9 and DDX21 as new biomarkers of colorectal cancer.
Title: RRP9 and DDX21 as new biomarkers of colorectal cancer.
Phase separation of DDX21 promotes colorectal cancer metastasis via MCM5-dependent EMT pathway.
Title: Phase separation of DDX21 promotes colorectal cancer metastasis via MCM5-dependent EMT pathway.
LINC00240 in the 6p22.1 risk locus promotes gastric cancer progression through USP10-mediated DDX21 stabilization.
Title: LINC00240 in the 6p22.1 risk locus promotes gastric cancer progression through USP10-mediated DDX21 stabilization.

Submit: New GeneRIF Correction See all GeneRIFs (45)

Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association scan of trait depression. EBI GWAS Catalog EBI GWAS CatalogPubMed

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
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 21 (DDX21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 21 (DDX21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 21 (DDX21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Pr55(Gag)	gag	Tandem affinity purification and mass spectrometry analysis identify DEAD (Asp-Glu-Ala-Asp) box helicase 21 (DDX21), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Rev	rev	DDX5 interacts with DDX21 and synergistically enhances the Rev function	PubMed
	rev	DDX21 interacts with HIV-1 Rev and enhances the Rev function. DDX21 partially co-localizes with Rev in the perinucleolar region	PubMed
Tat	tat	Interaction of HIV-1 Tat with RHII/Gu in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry	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

RH11523 (e-PCR)
- UniSTS:91934

G54121 (e-PCR)
- UniSTS:109358

RH93328 (e-PCR)
- UniSTS:87891

RH70628 (e-PCR)
- UniSTS:1917

RH44177 (e-PCR)
- UniSTS:38564

RH44765 (e-PCR)
- UniSTS:26053

DDX21__4686 (e-PCR)
- UniSTS:463581

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 7SK snRNA binding	IDA Inferred from Direct Assay more info	PubMed
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	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables RNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables RNA polymerase inhibitor activity	TAS Traceable Author Statement 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 double-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables mRNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables miRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables rRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables snoRNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in R-loop processing	IDA Inferred from Direct Assay more info	PubMed
involved_in chromatin looping	IEA Inferred from Electronic Annotation 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 negative regulation of transcription by RNA polymerase I	TAS Traceable Author Statement more info	PubMed
involved_in osteoblast differentiation	HDA more info	PubMed
involved_in positive regulation of canonical NF-kappaB signal transduction	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of myeloid dendritic cell cytokine production	IEA Inferred from Electronic Annotation more info
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	IDA Inferred from Direct Assay more info	PubMed
involved_in rRNA processing	IEA Inferred from Electronic Annotation more info
involved_in response to exogenous dsRNA	IEA Inferred from Electronic Annotation more info
involved_in transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of B-WICH complex	IDA Inferred from Direct Assay more info	PubMed
located_in chromosome	IDA Inferred from Direct Assay more info
located_in cytosol	ISS Inferred from Sequence or Structural Similarity more info
located_in membrane	HDA more info	PubMed
located_in mitochondrion	IEA Inferred from Electronic Annotation more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	NAS Non-traceable Author Statement more info	PubMed
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info

General protein information

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Preferred Names: nucleolar RNA helicase 2

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

NP_001243839.1

EC 3.6.4.13

NP_001397861.1

EC 3.6.4.13

NP_004719.2

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_001256910.2 → NP_001243839.1 nucleolar RNA helicase 2 isoform 2

See identical proteins and their annotated locations for NP_001243839.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) differs in the 5'UTR and has multiple coding region differences, compared to variant 1. These differences cause translation initiation at a downstream AUG and result in an isoform (2) with a shorter N-terminus, compared to isoform 1.

Source sequence(s)

AA446317, AL359844

Consensus CDS

CCDS73144.1

UniProtKB/TrEMBL

A0A8I5KND9

Related

ENSP00000480334.1, ENST00000620315.2

Conserved Domains (5) summary

PTZ00424
Location:100 → 486

PTZ00424; helicase 45; Provisional

cd00079
Location:343 → 470

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:120 → 327

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:549 → 641

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:650 → 703

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). ...
NM_001410932.1 → NP_001397861.1 nucleolar RNA helicase 2 isoform 3

Status: REVIEWED

Source sequence(s)

AL359844

Consensus CDS

CCDS91249.1

UniProtKB/TrEMBL

A0A8I5KNP3, A0A8I5KYZ4

Related

ENSP00000510328.1, ENST00000685106.1
NM_004728.4 → NP_004719.2 nucleolar RNA helicase 2 isoform 1

See identical proteins and their annotated locations for NP_004719.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longer isoform (1).

Source sequence(s)

AA446317, AL359844, BC008071, DW408689

Consensus CDS

CCDS31211.1

UniProtKB/Swiss-Prot

B2RDL0, Q13436, Q5VX41, Q68D35, Q9NR30

UniProtKB/TrEMBL

A0A8I5KNP3

Related

ENSP00000346120.4, ENST00000354185.9

Conserved Domains (3) summary

COG0513
Location:178 → 587

SrmB; Superfamily II DNA and RNA helicase [Replication, recombination and repair]

cd12936
Location:617 → 709

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:718 → 771

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). ...