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

Gene ID: 1660, updated on 5-Jul-2020

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
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

Genomic context

See DHX9 in Genome Data Viewer
Location:
1q25.3
Exon count:
29
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 1 NC_000001.11 (182839347..182887982)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (182808439..182857117)

Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene regulator of G protein signaling 8 Neighboring gene NSE4 homolog A, SMC5-SMC6 complex component pseudogene Neighboring gene N-acetylneuraminate pyruvate lyase Neighboring gene uncharacterized LOC647070 Neighboring gene SHC binding and spindle associated 1 like Neighboring gene RNA, 5S ribosomal pseudogene 71 Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 4

Genomic regions, transcripts, and products

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • FLJ17406

Gene Ontology Provided by GOA

Function Evidence Code Pubs
3'-5' DNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
3'-5' DNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
3'-5' DNA helicase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
3'-5' DNA/RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
3'-5' RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
ATP binding IDA
Inferred from Direct Assay
more info
PubMed 
ATPase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
ATPase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA binding ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA helicase activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
DNA helicase activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA replication origin binding IDA
Inferred from Direct Assay
more info
PubMed 
RISC complex binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA binding HDA PubMed 
RNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
RNA helicase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
RNA polymerase II complex binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II proximal promoter sequence-specific DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA polymerase II transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
RNA polymerase binding IDA
Inferred from Direct Assay
more info
PubMed 
RNA stem-loop binding IDA
Inferred from Direct Assay
more info
PubMed 
chromatin DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
double-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
importin-alpha family protein binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
mRNA binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
nucleoside-triphosphatase activity ISS
Inferred from Sequence or Structural Similarity
more info
 
nucleoside-triphosphate diphosphatase activity IDA
Inferred from Direct Assay
more info
PubMed 
polysome binding IDA
Inferred from Direct Assay
more info
PubMed 
promoter-specific chromatin binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
regulatory region RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
sequence-specific mRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
siRNA binding IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded DNA-dependent ATP-dependent 3'-5' DNA helicase activity IDA
Inferred from Direct Assay
more info
PubMed 
single-stranded RNA binding IDA
Inferred from Direct Assay
more info
PubMed 
transcription coactivator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
transcription coregulator activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
triplex DNA binding IDA
Inferred from Direct Assay
more info
PubMed 
Process Evidence Code Pubs
CRD-mediated mRNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA duplex unwinding IDA
Inferred from Direct Assay
more info
PubMed 
DNA duplex unwinding IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA duplex unwinding ISS
Inferred from Sequence or Structural Similarity
more info
 
DNA replication IEA
Inferred from Electronic Annotation
more info
 
DNA-templated transcription, termination IEA
Inferred from Electronic Annotation
more info
 
DNA-templated viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
G-quadruplex DNA unwinding IDA
Inferred from Direct Assay
more info
PubMed 
RNA secondary structure unwinding IDA
Inferred from Direct Assay
more info
PubMed 
alternative mRNA splicing, via spliceosome IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular protein-containing complex assembly IDA
Inferred from Direct Assay
more info
PubMed 
cellular response to exogenous dsRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
cellular response to tumor necrosis factor IMP
Inferred from Mutant Phenotype
more info
PubMed 
inflammatory response IEA
Inferred from Electronic Annotation
more info
 
innate immune response IEA
Inferred from Electronic Annotation
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
mRNA transport IEA
Inferred from Electronic Annotation
more info
 
osteoblast differentiation HDA PubMed 
positive regulation of DNA repair IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA replication IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of NF-kappaB transcription factor activity IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of RNA export from nucleus IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of cytoplasmic translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of fibroblast proliferation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of gene silencing by miRNA IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of inflammatory response ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of innate immune response ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interferon-alpha secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interferon-beta secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of interleukin-18 production ISS
Inferred from Sequence or Structural Similarity
more info
 
positive regulation of interleukin-6 secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of polysome binding IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of response to cytokine stimulus IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of transcription by RNA polymerase II IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of tumor necrosis factor secretion IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of type I interferon production TAS
Traceable Author Statement
more info
 
positive regulation of viral transcription IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of viral translation IMP
Inferred from Mutant Phenotype
more info
PubMed 
protein localization to cytoplasmic stress granule IMP
Inferred from Mutant Phenotype
more info
PubMed 
pyroptosis ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of cytoplasmic translation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of defense response to virus by host ISS
Inferred from Sequence or Structural Similarity
more info
 
regulation of mRNA processing IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of mRNA processing IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IMP
Inferred from Mutant Phenotype
more info
PubMed 
rhythmic process IEA
Inferred from Electronic Annotation
more info
 
small RNA loading onto RISC IMP
Inferred from Mutant Phenotype
more info
PubMed 
targeting of mRNA for destruction involved in RNA interference IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
RISC complex IDA
Inferred from Direct Assay
more info
PubMed 
RISC-loading complex IMP
Inferred from Mutant Phenotype
more info
PubMed 
actin cytoskeleton IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
intracellular IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
membrane HDA PubMed 
nuclear body IDA
Inferred from Direct Assay
more info
PubMed 
nuclear stress granule IDA
Inferred from Direct Assay
more info
PubMed 
nuclear stress granule IMP
Inferred from Mutant Phenotype
more info
PubMed 
nucleolus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleoplasm IDA
Inferred from Direct Assay
more info
PubMed 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
nucleus IDA
Inferred from Direct Assay
more info
PubMed 
perichromatin fibrils IDA
Inferred from Direct Assay
more info
PubMed 
polysomal ribosome IDA
Inferred from Direct Assay
more info
PubMed 
polysome IDA
Inferred from Direct Assay
more info
PubMed 
protein-containing complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
ribonucleoprotein complex IMP
Inferred from Mutant Phenotype
more info
PubMed 

General protein information

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

NCBI Reference Sequences (RefSeq)

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

  1. NG_029930.1 RefSeqGene

    Range
    5001..53679
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001357.5NP_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
    Q08211
    UniProtKB/TrEMBL
    B3KU66
    Related
    ENSP00000356520.3, ENST00000367549.4
    Conserved Domains (2) summary
    smart00358
    Location:569
    DSRM; Double-stranded RNA binding motif
    COG1643
    Location:3811095
    HrpA; HrpA-like RNA helicase [Translation, ribosomal structure and biogenesis]

RNA

  1. 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: Homo sapiens Updated Annotation Release 109.

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000001.11 Reference GRCh38.p13 Primary Assembly

    Range
    182839347..182887982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. 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.
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