DHX9 DExH-box helicase 9 [Homo sapiens (human)] - Gene

Summary

Official Symbol: DHX9provided by HGNC
Official Full Name: DExH-box helicase 9provided by HGNC
Primary source: HGNC:HGNC:2750
See related: Ensembl:ENSG00000135829 MIM:603115; AllianceGenome:HGNC:2750
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: LKP; RHA; DDX9; NDH2; NDHII
Summary: This gene encodes a member of the DEAH-containing family of RNA helicases. The encoded protein is an enzyme that catalyzes the ATP-dependent unwinding of double-stranded RNA and DNA-RNA complexes. This protein localizes to both the nucleus and the cytoplasm and functions as a transcriptional regulator. This protein may also be involved in the expression and nuclear export of retroviral RNAs. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on chromosomes 11 and 13.[provided by RefSeq, Feb 2010]
Expression: Ubiquitous expression in bone marrow (RPKM 54.5), testis (RPKM 36.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q25.3

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (182839347..182887982)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (182198510..182247148)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (182808482..182857117)

Chromosome 1 - NC_000001.11 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: 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?

Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells.
Title: Induction of Viral Mimicry Upon Loss of DHX9 and ADAR1 in Breast Cancer Cells.
AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer.
Title: AKT1 interacts with DHX9 to Mitigate R Loop-Induced Replication Stress in Ovarian Cancer.
Complex interplay between FMRP and DHX9 during DNA replication stress.
Title: Complex interplay between FMRP and DHX9 during DNA replication stress.
DHX9 Strengthens Atherosclerosis Progression By Promoting Inflammation in Macrophages.
Title: DHX9 Strengthens Atherosclerosis Progression By Promoting Inflammation in Macrophages.
ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress.
Title: ATR phosphorylates DHX9 at serine 321 to suppress R-loop accumulation upon genotoxic stress.
The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma.
Title: The DNA/RNA helicase DHX9 orchestrates the KDM2B-mediated transcriptional regulation of YAP1 in Ewing sarcoma.
Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9.
Title: Development of assays to support identification and characterization of modulators of DExH-box helicase DHX9.
Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease.
Title: Monoallelic variation in DHX9, the gene encoding the DExH-box helicase DHX9, underlies neurodevelopment disorders and Charcot-Marie-Tooth disease.
Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences.
Title: Heterozygous loss-of-function DHX9 variants are associated with neurodevelopmental disorders: Human genetic and experimental evidences.
The DHX9 helicase interacts with human DNA polymerase delta4 and stimulates its activity in D-loop extension synthesis.
Title: The DHX9 helicase interacts with human DNA polymerase δ4 and stimulates its activity in D-loop extension synthesis.

Submit: New GeneRIF Correction See all GeneRIFs (86)

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)

HIV-1 interactions

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Replication interactions

Interaction	Pubs
HIV-1 infectivity is enhanced by DHX9 (RHA) binding to the primer binding site (PBS)-segment of dimeric HIV-1 5'-UTR	PubMed

Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	Tandem affinity purification and mass spectrometry analysis identify ATP-dependent RNA helicase A (RHA, DHX9), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Gag-Pol	gag-pol	HIV-1 Gag-Pol polyprotein is reduced by siRNA-mediated RHA (DHX9) downregulation, suggesting that RHA regulates Gag-Pol expression	PubMed
	gag-pol	Tandem affinity purification and mass spectrometry analysis identify ATP-dependent RNA helicase A (RHA, DHX9), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
Nef	nef	HIV-1 Nef is reduced by siRNA-mediated RHA (DHX9) downregulation, suggesting that RHA regulates Nef expression	PubMed
	nef	Tandem affinity purification and mass spectrometry analysis identify ATP-dependent RNA helicase A (RHA, DHX9), 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 ATP-dependent RNA helicase A (RHA, DHX9), HIV-1 Gag, Gag/Pol, gp120, and Nef incorporated into Staufen1 RNP complexes isolated from HIV-1-expressing cells	PubMed
	gag	HIV-1 RU5 is necessary for post-transcriptional control element (PCE) activity and interaction with Dhx9/RNA helicase A (RHA). RHA is necessary for efficient production of HIV-1 Gag	PubMed
	gag	HIV-1 Gag interacts with RNA helicase A (RHA) in an RNA-dependent manner, and RHA binds HIV-1 RNA	PubMed
Rev	rev	HIV-1 Rev is reduced by siRNA-mediated RHA (DHX9) downregulation, suggesting that RHA regulates Rev expression	PubMed
	rev	RNA helicase A is a cofactor that binds to the Rev responsive element (RRE) of HIV-1 mRNA during Rev-mediated nuclear export of mRNA	PubMed
	rev	HIV-1 Rev interacting protein, DEAH (Asp-Glu-Ala-His) box polypeptide 9 (DHX9), is identified by the in-vitro binding experiments involving cytosolic or nuclear extracts from HeLa cells. The interaction of Rev with DHX9 is increased by RRE	PubMed
Tat	tat	Interaction of HIV-1 Tat with RHA in T-cells is identified by a proteomic strategy based on affinity chromatography coupled with mass spectrometry	PubMed
Vif	vif	HIV-1 Vif is reduced by siRNA-mediated RHA downregulation, suggesting that RHA regulates Vif expression	PubMed
reverse transcriptase	gag-pol	HIV-1 RT p66 is reduced by siRNA-mediated RHA downregulation, suggesting that RHA regulates RT p66 expression	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

G32727 (e-PCR)
- UniSTS:117309

NoName (e-PCR)
- UniSTS:483662

RH17975 (e-PCR)
- UniSTS:31835

AL033692 (e-PCR)
- UniSTS:93551

RH69013 (e-PCR)
- UniSTS:14729

D1S2238 (e-PCR)
- UniSTS:46738

SHGC-57619 (e-PCR)
- UniSTS:57237

RH48886 (e-PCR)
- UniSTS:74912

D1S1703 (e-PCR)
- UniSTS:76193

D13S1668 (e-PCR)
- UniSTS:62630

D1S3440 (e-PCR)
- UniSTS:3520

A009P09 (e-PCR)
- UniSTS:55249

AL033994 (e-PCR)
- UniSTS:93410

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables 3'-5' DNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 3'-5' DNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3'-5' DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 3'-5' DNA/RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables 3'-5' RNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables ATP binding	IDA Inferred from Direct Assay more info	PubMed
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA helicase activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables DNA replication origin binding	IDA Inferred from Direct Assay more info	PubMed
enables RISC complex binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA binding	HDA more info	PubMed
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	IDA Inferred from Direct Assay 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	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II complex binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA polymerase II-specific DNA-binding transcription factor binding	IPI Inferred from Physical Interaction more info	PubMed
enables RNA polymerase binding	IDA Inferred from Direct Assay more info	PubMed
enables RNA stem-loop binding	IDA Inferred from Direct Assay more info	PubMed
enables chromatin DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables double-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables importin-alpha family protein binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables mRNA binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleoside triphosphate diphosphatase activity	IDA Inferred from Direct Assay more info	PubMed
enables promoter-specific chromatin binding	IMP Inferred from Mutant Phenotype more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables regulatory region RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables ribonucleoside triphosphate phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ribosome binding	IDA Inferred from Direct Assay more info	PubMed
enables sequence-specific mRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables siRNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded 3'-5' DNA helicase activity	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables single-stranded RNA binding	IDA Inferred from Direct Assay more info	PubMed
enables transcription coactivator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables transcription coregulator activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables triplex DNA binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in CRD-mediated mRNA stabilization	IDA Inferred from Direct Assay more info	PubMed
involved_in CRD-mediated mRNA stabilization	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA duplex unwinding	IDA Inferred from Direct Assay more info	PubMed
involved_in DNA duplex unwinding	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in DNA duplex unwinding	ISS Inferred from Sequence or Structural Similarity more info
involved_in DNA replication	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated transcription termination	IEA Inferred from Electronic Annotation more info
involved_in DNA-templated viral transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in G-quadruplex DNA unwinding	IDA Inferred from Direct Assay more info	PubMed
involved_in RISC complex assembly	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in RNA secondary structure unwinding	IDA Inferred from Direct Assay more info	PubMed
involved_in alternative mRNA splicing, via spliceosome	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to exogenous dsRNA	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to tumor necrosis factor	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in innate immune response	IEA Inferred from Electronic Annotation more info
involved_in mRNA transport	IEA Inferred from Electronic Annotation more info
involved_in miRNA-mediated post-transcriptional gene silencing	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay	IDA Inferred from Direct Assay more info	PubMed
involved_in osteoblast differentiation	HDA more info	PubMed
involved_in positive regulation of DNA repair	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA replication	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of NF-kappaB transcription factor activity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of RNA export from nucleus	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cytoplasmic translation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of cytoplasmic translation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of fibroblast proliferation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of inflammatory response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of innate immune response	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interferon-alpha production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interferon-beta production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of interleukin-18 production	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of interleukin-6 production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of response to cytokine stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of tumor necrosis factor production	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in positive regulation of viral transcription	IDA Inferred from Direct Assay more info	PubMed
involved_in protein localization to cytoplasmic stress granule	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in protein-containing complex assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in pyroptosis	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of cytoplasmic translation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of defense response to virus by host	ISS Inferred from Sequence or Structural Similarity more info
involved_in regulation of mRNA processing	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of mRNA processing	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of transcription by RNA polymerase II	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in rhythmic process	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of CRD-mediated mRNA stability complex	IDA Inferred from Direct Assay more info	PubMed
part_of CRD-mediated mRNA stability complex	IPI Inferred from Physical Interaction more info	PubMed
part_of RISC complex	IDA Inferred from Direct Assay more info	PubMed
part_of RISC-loading complex	IMP Inferred from Mutant Phenotype more info	PubMed
located_in actin cytoskeleton	IDA Inferred from Direct Assay more info	PubMed
located_in centrosome	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytoplasmic ribonucleoprotein granule	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	TAS Traceable Author Statement more info
is_active_in intracellular anatomical structure	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	HDA more info	PubMed
located_in nuclear body	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear stress granule	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear stress granule	IMP Inferred from Mutant Phenotype 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
located_in nucleoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in nucleoplasm	TAS Traceable Author Statement more info
located_in nucleus	IDA Inferred from Direct Assay more info	PubMed
located_in perichromatin fibrils	IDA Inferred from Direct Assay more info	PubMed
part_of protein-containing complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ribonucleoprotein complex	IDA Inferred from Direct Assay more info	PubMed
part_of ribonucleoprotein complex	IMP Inferred from Mutant Phenotype more info	PubMed

General protein information

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Preferred Names: ATP-dependent RNA helicase A

Names: DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9; DEAH (Asp-Glu-Ala-His) box helicase 9; DEAH (Asp-Glu-Ala-His) box polypeptide 9; DEAH box protein 9; DEAH-box helicase 9; RNA helicase A; leukophysin; nuclear DNA helicase II

NP_001348.2

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.

Genomic

NG_029930.2 RefSeqGene

Range

5002..53637

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001357.5 → NP_001348.2 ATP-dependent RNA helicase A

See identical proteins and their annotated locations for NP_001348.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the functional protein.

Source sequence(s)

AL355999, AL662837

Consensus CDS

CCDS41444.1

UniProtKB/Swiss-Prot

B2RNV4, Q05CI5, Q08211, Q12803, Q32Q22, Q5VY62, Q6PD69, Q99556

Related

ENSP00000356520.3, ENST00000367549.4

Conserved Domains (2) summary

smart00358
Location:5 → 69

DSRM; Double-stranded RNA binding motif

COG1643
Location:381 → 1095

HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

RNA

NR_033302.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (2) has an additional internal exon, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most supported/expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL355999, AL662837

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

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

182839347..182887982

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

182198510..182247148

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_030588.1: Suppressed sequence

Description

NM_030588.1: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.