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DHX9 DEAH (Asp-Glu-Ala-His) box helicase 9 [ Homo sapiens (human) ]

Gene ID: 1660, updated on 11-Sep-2014
Official Symbol
DHX9provided by HGNC
Official Full Name
DEAH (Asp-Glu-Ala-His) box helicase 9provided by HGNC
Primary source
HGNC:HGNC:2750
See related
Ensembl:ENSG00000135829; HPRD:04386; MIM:603115; Vega:OTTHUMG00000035337
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]
See DHX9 in Epigenomics, MapViewer
Location:
1q25
Exon count:
29
Annotation release Status Assembly Chr Location
106 current GRCh38 (GCF_000001405.26) 1 NC_000001.11 (182839304..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 non-SMC element 4 homolog A (S. cerevisiae) pseudogene Neighboring gene N-acetylneuraminate pyruvate lyase (dihydrodipicolinate synthase) Neighboring gene SHC SH2-domain binding protein 1-like Neighboring gene natural cytotoxicity triggering receptor 1 pseudogene Neighboring gene high mobility group nucleosome binding domain 1 pseudogene 4

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

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 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 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 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
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
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

Go to the HIV-1, Human Interaction Database

  • Activated TLR4 signalling, organism-specific biosystem (from REACTOME)
    Activated TLR4 signalling, organism-specific biosystemTLR4 is unique among the TLR family in its ability to recruit four adapters to activate two distinct signaling pathways. One pathway is activated by the pair of the adapters Mal or TIRAP (Toll/inter...
  • Cytosolic sensors of pathogen-associated DNA, organism-specific biosystem (from REACTOME)
    Cytosolic sensors of pathogen-associated DNA, organism-specific biosystemPresence of pathogen-associated DNA in cytosol induces type I IFN production. Several intracellular receptors have been implicated to some degree. These include DNA-dependent activator of interferon ...
  • DEx/H-box helicases activate type I IFN and inflammatory cytokines production, organism-specific biosystem (from REACTOME)
    DEx/H-box helicases activate type I IFN and inflammatory cytokines production, organism-specific biosystemDHX36 and DHX9 are aspartate-glutamate-any amino acid aspartate/histidine (DExD/H) box helicase (DHX) proteins that localize in the cytosol. The DHX RNA helicases family includes a large number of pr...
  • Gene Expression, organism-specific biosystem (from REACTOME)
    Gene Expression, organism-specific biosystemGene Expression covers the pathways by which genomic DNA is transcribed to yield RNA, the regulation of these transcription processes, and the pathways by which newly-made RNA Transcripts are process...
  • Immune System, organism-specific biosystem (from REACTOME)
    Immune System, organism-specific biosystemHumans are exposed to millions of potential pathogens daily, through contact, ingestion, and inhalation. Our ability to avoid infection depends on the adaptive immune system and during the first crit...
  • Innate Immune System, organism-specific biosystem (from REACTOME)
    Innate Immune System, organism-specific biosystemInnate immunity encompases the nonspecific part of immunity tha are part of an individual's natural biologic makeup
  • MyD88 cascade initiated on plasma membrane, organism-specific biosystem (from REACTOME)
    MyD88 cascade initiated on plasma membrane, organism-specific biosystemMammalian myeloid differentiation factor 88 (MyD88) is Toll/interleukin (IL)-1 (TIR)-domain containing adapter protein which plays crucial role in TLR signaling. All TLRs, with only one exception of...
  • MyD88 dependent cascade initiated on endosome, organism-specific biosystem (from REACTOME)
    MyD88 dependent cascade initiated on endosome, organism-specific biosystemUpon binding of their ligands, TLR7/8 and TLR9 recruit a cytoplasmic adaptor MyD88 and IRAKs, downstream of which the signaling pathways are divided to induce either inflammatory cytokines or type I ...
  • MyD88-independent cascade, organism-specific biosystem (from REACTOME)
    MyD88-independent cascade, organism-specific biosystemMyD88-independent signaling pathway is shared by TLR3 and TLR4 cascades. TIR-domain-containing adapter-inducing interferon-beta (TRIF or TICAM1) is a key adapter molecule in transducing signals from ...
  • MyD88:Mal cascade initiated on plasma membrane, organism-specific biosystem (from REACTOME)
    MyD88:Mal cascade initiated on plasma membrane, organism-specific biosystemThe first known downstream component of TLR4 and TLR2 signaling is the adaptor MyD88. Another adapter MyD88-adaptor-like (Mal; also known as TIR-domain-containing adaptor protein or TIRAP) has also b...
  • Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystem (from REACTOME)
    Processing of Capped Intron-Containing Pre-mRNA, organism-specific biosystemCo-transcriptional pre-mRNA splicing is not obligatory. Pre-mRNA splicing begins co-transcriptionally and often continues post-transcriptionally. Human genes contain an average of nine introns per ge...
  • RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystem (from REACTOME)
    RIG-I/MDA5 mediated induction of IFN-alpha/beta pathways, organism-specific biosystemRIG-I-like helicases (RLHs) the retinoic acid inducible gene-I (RIG-I) and melanoma differentiation associated gene 5 (MDA5) are RNA helicases that recognize viral RNA present within the cytoplasm. F...
  • RIP-mediated NFkB activation via ZBP1, organism-specific biosystem (from REACTOME)
    RIP-mediated NFkB activation via ZBP1, organism-specific biosystemOverexpression of human or murine ZBP1 (DAI) in human embryonic kidney 293T cells (HEK293T) activated NF-kB-dependent promoter in a dose-dependent manner. Two RHIM-contaning kinases RIP1 and RIP3 are...
  • TAK1 activates NFkB by phosphorylation and activation of IKKs complex, organism-specific biosystem (from REACTOME)
    TAK1 activates NFkB by phosphorylation and activation of IKKs complex, organism-specific biosystemNF-kappaB is sequestered in the cytoplasm in a complex with inhibitor of NF-kappaB (IkB). Almost all NF-kappaB activation pathways are mediated by IkB kinase (IKK), which phosphorylates IkB resulting...
  • TRAF6 mediated NF-kB activation, organism-specific biosystem (from REACTOME)
    TRAF6 mediated NF-kB activation, organism-specific biosystemThe TRAF6/TAK1 signal activates a canonical IKK complex, resulting in the activation of NF-kB as well as MAPK cascades leading to the activation of AP-1. Although TRAF6/TAK1 has been implicated in To...
  • TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation, organism-specific biosystem (from REACTOME)
    TRAF6 mediated induction of NFkB and MAP kinases upon TLR7/8 or 9 activation, organism-specific biosystemTRAF6 mediates NFkB activation via canonical phosphorylation of IKK complex by TAK1. TRAF6 and TAK1 also regulate MAPK cascades leading to the activation of AP-1.
  • TRIF-mediated TLR3/TLR4 signaling, organism-specific biosystem (from REACTOME)
    TRIF-mediated TLR3/TLR4 signaling, organism-specific biosystemTRIF(TICAM1) was shown to induce IRF3/7 and NF-?B activation and apoptosis through distinct intracellular signaling pathways [Han KJ et al 2004; Kaiser WJ and Offermann MK et al 2005]. TRIF consists...
  • Toll Like Receptor 10 (TLR10) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 10 (TLR10) Cascade, organism-specific biosystemLittle is known about TLR10 ligands. It has been established that the receptor homodimerizes upon binding and signals in an MyD88-dependent manner (Hasan U et al 2005; Nyman T et al 2008). It may als...
  • Toll Like Receptor 2 (TLR2) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 2 (TLR2) Cascade, organism-specific biosystemTLR2 is involved in recognition of peptidoglycan from gram-positive bacteria, bacterial lipoproteins, mycoplasma lipoprotein and mycobacterial products. It is quite possible that recognition of at le...
  • Toll Like Receptor 3 (TLR3) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 3 (TLR3) Cascade, organism-specific biosystemToll-like receptor 3 (TLR3) as was shown for mammals is expressed on myeloid dendritic cells, respiratory epithelium, macrophages, and appears to play a central role in mediating the antiviral and in...
  • Toll Like Receptor 4 (TLR4) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 4 (TLR4) Cascade, organism-specific biosystemToll-like Receptor 4 is a Microbe Associated Molecular Pattern receptor well known for it's sensitivity to Bacterial Lipopolysaccharides (LPS). LPS is assembled within diverse Gram-negative bacteria,...
  • Toll Like Receptor 5 (TLR5) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 5 (TLR5) Cascade, organism-specific biosystemTLR5 is the receptor for flagellin, the protein that forms bacterial flagella. Unlike most other Pathogen-Associated Molecular Patterns (PAMPs), flagellin does not undergo any posttranslational modif...
  • Toll Like Receptor 7/8 (TLR7/8) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 7/8 (TLR7/8) Cascade, organism-specific biosystemRNA can serve as a danger signal, both in its double-stranded form (that is associated with viral infection), as well as single-stranded RNA (ssRNA). Specifically, guanosine (G)- and uridine (U)-rich...
  • Toll Like Receptor 9 (TLR9) Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor 9 (TLR9) Cascade, organism-specific biosystemCpG DNA is an unusual Pathogen-Associated Molecular Pattern (PAMP). Cytosine methylation exists in mammalian but not bacterial cells, and most (but not all) CpG in the mammalian genome is methylated....
  • Toll Like Receptor TLR1:TLR2 Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor TLR1:TLR2 Cascade, organism-specific biosystemTLR1 is expressed by monocytes. TLR1 and TLR2 cotranslationally form heterodimeric complexes on the cell surface and in the cytosol. The TLR2:TLR1 complex recognizes Neisserial PorB and Mycobacterial...
  • Toll Like Receptor TLR6:TLR2 Cascade, organism-specific biosystem (from REACTOME)
    Toll Like Receptor TLR6:TLR2 Cascade, organism-specific biosystemTLR2 and TLR4 recognize different bacterial cell wall components. While TLR4 is trained onto Gram-negative lipopolysaccharide components, TLR2 - in combination with TLR6 - plays a major role in recog...
  • Toll-Like Receptors Cascades, organism-specific biosystem (from REACTOME)
    Toll-Like Receptors Cascades, organism-specific biosystemIn human, ten members of the Toll-like receptor (TLR) family (TLR1-TLR10) have been identified (TLR11 has been found in mouse, but not in human). All TLRs have a similar Toll/IL-1 receptor (TIR) doma...
  • ZBP1(DAI) mediated induction of type I IFNs, organism-specific biosystem (from REACTOME)
    ZBP1(DAI) mediated induction of type I IFNs, organism-specific biosystemZ-DNA-binding protein-1 (ZBP1), also known as, DNA-dependent activator of IFN-regulatory factors (DAI) was reported to initiate innate immune responses in murine L929 cells upon stimulation by multip...
  • mRNA Splicing, organism-specific biosystem (from REACTOME)
    mRNA Splicing, organism-specific biosystemThe process in which excision of introns from the primary transcript of messenger RNA (mRNA) is followed by ligation of the two exon termini exposed by removal of each intron, is called mRNA splicing...
  • mRNA Splicing - Major Pathway, organism-specific biosystem (from REACTOME)
    mRNA Splicing - Major Pathway, organism-specific biosystemThe splicing of pre-mRNA occurs within a large, very dynamic complex, designated the 'spliceosome'. The 50-60S spliceosomes are estimated to be 40-60 nm in diameter, and have molecular weights in the...
  • mRNA processing, organism-specific biosystem (from WikiPathways)
    mRNA processing, organism-specific biosystemThis process describes the conversion of precursor messenger RNA into mature messenger RNA (mRNA). The pre-mRNA molecule undergoes three main modifications. These modifications are 5' capping, 3' po...
Products Interactant Other Gene Complex Source Pubs Description

Markers

Homology

Clone Names

  • FLJ17406

Gene Ontology Provided by GOA

Function Evidence Code Pubs
ATP binding IEA
Inferred from Electronic Annotation
more info
 
ATP-dependent DNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
ATP-dependent RNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
DNA binding IEA
Inferred from Electronic Annotation
more info
 
RNA helicase activity TAS
Traceable Author Statement
more info
PubMed 
RNA polymerase II transcription factor binding IPI
Inferred from Physical Interaction
more info
PubMed 
poly(A) RNA binding IDA
Inferred from Direct Assay
more info
 
protein binding IPI
Inferred from Physical Interaction
more info
PubMed 
Process Evidence Code Pubs
ATP catabolic process IEA
Inferred from Electronic Annotation
more info
 
ATP catabolic process TAS
Traceable Author Statement
more info
PubMed 
CRD-mediated mRNA stabilization IMP
Inferred from Mutant Phenotype
more info
PubMed 
DNA duplex unwinding TAS
Traceable Author Statement
more info
PubMed 
RNA splicing TAS
Traceable Author Statement
more info
 
cellular response to heat IEA
Inferred from Electronic Annotation
more info
 
circadian rhythm IEA
Inferred from Electronic Annotation
more info
 
gene expression TAS
Traceable Author Statement
more info
 
innate immune response TAS
Traceable Author Statement
more info
 
mRNA splicing, via spliceosome TAS
Traceable Author Statement
more info
 
osteoblast differentiation IDA
Inferred from Direct Assay
more info
PubMed 
positive regulation of type I interferon production TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
CRD-mediated mRNA stability complex IDA
Inferred from Direct Assay
more info
PubMed 
centrosome IDA
Inferred from Direct Assay
more info
PubMed 
cytoplasm TAS
Traceable Author Statement
more info
PubMed 
cytoplasmic ribonucleoprotein granule IDA
Inferred from Direct Assay
more info
PubMed 
cytosol TAS
Traceable Author Statement
more info
 
membrane IDA
Inferred from Direct Assay
more info
PubMed 
nucleolus IDA
Inferred from Direct Assay
more info
 
NOT nucleolus IDA
Inferred from Direct Assay
more info
 
nucleoplasm TAS
Traceable Author Statement
more info
 
nucleus IDA
Inferred from Direct Assay
more info
 
ribonucleoprotein complex IDA
Inferred from Direct Assay
more info
PubMed 
Preferred Names
ATP-dependent RNA helicase A
Names
ATP-dependent RNA helicase A
leukophysin
RNA helicase A
DEAH box protein 9
nuclear DNA helicase II
DEAH (Asp-Glu-Ala-His) box polypeptide 9
DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 9
NP_001348.2

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 

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

mRNA and Protein(s)

  1. NM_001357.4NP_001348.2  ATP-dependent RNA helicase A

    See proteins identical to NP_001348.2

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the functional protein.
    Source sequence(s)
    AA836637, AK096582, BC137136, DB223823
    Consensus CDS
    CCDS41444.1
    UniProtKB/TrEMBL
    B3KU66
    UniProtKB/Swiss-Prot
    Q08211
    Related
    ENSP00000356520, OTTHUMP00000033287, ENST00000367549, OTTHUMT00000085522
    Conserved Domains (6) summary
    COG1643
    Location:3811095
    HrpA; HrpA-like helicases [DNA replication, recombination, and repair]
    cd00046
    Location:405546
    DEXDc; DEAD-like helicases superfamily. A diverse family of proteins involved in ATP-dependent RNA or DNA unwinding. This domain contains the ATP-binding region.
    cd00048
    Location:369
    DSRM; Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, ...
    cd00079
    Location:631776
    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 ...
    pfam04408
    Location:831919
    HA2; Helicase associated domain (HA2)
    pfam07717
    Location:9591073
    OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RNA

  1. NR_033302.1 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)
    AA836637, AK226102, AL355999, DB223823

RefSeqs of Annotated Genomes: Homo sapiens Annotation Release 106

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

Reference GRCh38 Primary Assembly

Genomic

  1. NC_000001.11 

    Range
    182839304..182887982
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate HuRef

Genomic

  1. AC_000133.1 

    Range
    154044114..154092793
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate CHM1_1.1

Genomic

  1. NC_018912.2 

    Range
    184231696..184280375
    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.