Human Gene DHX9 (uc001gpr.3) Description and Page Index
  Description: Homo sapiens DEAH (Asp-Glu-Ala-His) box helicase 9 (DHX9), transcript variant 1, mRNA.
RefSeq Summary (NM_001357): 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].
Transcript (Including UTRs)
   Position: hg19 chr1:182,808,439-182,857,117 Size: 48,679 Total Exon Count: 28 Strand: +
Coding Region
   Position: hg19 chr1:182,811,702-182,856,569 Size: 44,868 Coding Exon Count: 27 

Page IndexSequence and LinksUniProtKB CommentsGenetic AssociationsMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
Genomic Sequence (chr1:182,808,439-182,857,117)mRNA (may differ from genome)Protein (1270 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
BioGPSCGAPEnsemblEntrez GeneExonPrimerGeneCards
neXtProtOMIMPubMedReactomeStanford SOURCETreefam

-  Comments and Description Text from UniProtKB
DESCRIPTION: RecName: Full=ATP-dependent RNA helicase A; Short=RHA; EC=; AltName: Full=DEAH box protein 9; AltName: Full=Leukophysin; Short=LKP; AltName: Full=Nuclear DNA helicase II; Short=NDH II;
FUNCTION: Unwinds double-stranded DNA and RNA in a 3' to 5' direction. Alteration of secondary structure may subsequently influence interactions with proteins or other nucleic acids. Functions as a transcriptional activator. Component of the CRD- mediated complex that promotes MYC mRNA stability. Involved with LARP6 in the stabilization of type I collagen mRNAs for CO1A1 and CO1A2.
CATALYTIC ACTIVITY: ATP + H(2)O = ADP + phosphate.
SUBUNIT: Interacts with ZIC2 (By similarity). Component of the coding region determinant (CRD)-mediated complex, composed of DHX9, HNRNPU, IGF2BP1, SYNCRIP and YBX1. Identified in a mRNP complex, at least composed of DHX9, DDX3X, ELAVL1, HNRNPU, IGF2BP1, ILF3, PABPC1, PCBP2, PTBP2, STAU1, STAU2, SYNCRIP and YBX1. Identified in a mRNP granule complex, at least composed of ACTB, ACTN4, DHX9, ERG, HNRNPA1, HNRNPA2B1, HNRNPAB, HNRNPD, HNRNPL, HNRNPR, HNRNPU, HSPA1, HSPA8, IGF2BP1, ILF2, ILF3, NCBP1, NCL, PABPC1, PABPC4, PABPN1, RPLP0, RPS3, RPS3A, RPS4X, RPS8, RPS9, SYNCRIP, TROVE2, YBX1 and untranslated mRNAs. Interacts with IGF2BP1. Binds MBD2, HRMT1L2/PRMT1, and RELA. May act to directly link BRCA1, CREBBP or SMN1 and the RNA polymerase II complex. Can also interact with XRCC5 and with TOP2A in an RNA dependent manner; these interactions may be indirect. Interaction with TOP2A is promoted by UBC9. Interacts with histone H2AFX and this requires phosphorylation of H2AFX on 'Ser-139'. Interacts with LARP6.
INTERACTION: P19525:EIF2AK2; NbExp=2; IntAct=EBI-352022, EBI-640775; Q9UBU9:NXF1; NbExp=7; IntAct=EBI-352022, EBI-398874; Q99873:PRMT1; NbExp=2; IntAct=EBI-352022, EBI-78738; Q04206:RELA; NbExp=4; IntAct=EBI-352022, EBI-73886;
SUBCELLULAR LOCATION: Nucleus, nucleolus. Cytoplasm. Note=Localized in cytoplasmic mRNP granules containing untranslated mRNAs. Can shuttle between nucleus and cytoplasm.
DOMAIN: The MTAD domain mediates interaction with the RNA polymerase II holoenzyme. The NTD domain is necessary and sufficient for nucleo-cytoplasmic shuttling and interaction with HRMT1L2 and SMN1.
PTM: Methylated. HRMT1L2 mediated methylation of undefined Arg residues in the NTD is required for nuclear localization.
PTM: May be phosphorylated by PRKDC/XRCC7. Phosphorylated upon DNA damage, probably by ATM or ATR.
SIMILARITY: Belongs to the DEAD box helicase family. DEAH subfamily.
SIMILARITY: Contains 2 DRBM (double-stranded RNA-binding) domains.
SIMILARITY: Contains 1 helicase ATP-binding domain.
SIMILARITY: Contains 1 helicase C-terminal domain.

-  Genetic Association Studies of Complex Diseases and Disorders
  Genetic Association Database (archive): DHX9
CDC HuGE Published Literature: DHX9

-  MalaCards Disease Associations
  MalaCards Gene Search: DHX9
Diseases sorted by gene-association score: pseudopterygium (17), werner syndrome (12), conjunctival degeneration (9), endometriosis of uterus (9), hypopyon (7), corneal ulcer (6)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 42.93 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1197.00 RPKM

View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -53.60175-0.306 Picture PostScript Text
3' UTR -114.60548-0.209 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR011545 - DNA/RNA_helicase_DEAD/DEAH_N
IPR002464 - DNA/RNA_helicase_DEAH_CS
IPR001159 - Ds-RNA-bd
IPR014720 - dsRNA-bd-like
IPR011709 - DUF1605
IPR007502 - Helicase-assoc_dom
IPR014001 - Helicase_ATP-bd
IPR001650 - Helicase_C

Pfam Domains:
PF00035 - Double-stranded RNA binding motif
PF00270 - DEAD/DEAH box helicase
PF00271 - Helicase conserved C-terminal domain
PF04408 - Helicase associated domain (HA2)
PF07717 - Oligonucleotide/oligosaccharide-binding (OB)-fold

SCOP Domains:
52540 - P-loop containing nucleoside triphosphate hydrolases
54768 - dsRNA-binding domain-like

Protein Data Bank (PDB) 3-D Structure
MuPIT help

- X-ray MuPIT

ModBase Predicted Comparative 3D Structure on Q08211
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologGenome BrowserGenome BrowserGenome BrowserNo ortholog
Gene Details  Gene DetailsGene Details 
Gene Sorter  Gene SorterGene Sorter 
  Protein SequenceProtein SequenceProtein Sequence 

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0000993 RNA polymerase II core binding
GO:0001047 core promoter binding
GO:0001069 regulatory region RNA binding
GO:0001085 RNA polymerase II transcription factor binding
GO:0001104 RNA polymerase II transcription cofactor activity
GO:0001105 RNA polymerase II transcription coactivator activity
GO:0003676 nucleic acid binding
GO:0003677 DNA binding
GO:0003688 DNA replication origin binding
GO:0003690 double-stranded DNA binding
GO:0003697 single-stranded DNA binding
GO:0003723 RNA binding
GO:0003724 RNA helicase activity
GO:0003725 double-stranded RNA binding
GO:0003727 single-stranded RNA binding
GO:0003729 mRNA binding
GO:0004003 ATP-dependent DNA helicase activity
GO:0004004 ATP-dependent RNA helicase activity
GO:0004386 helicase activity
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016787 hydrolase activity
GO:0016887 ATPase activity
GO:0017111 nucleoside-triphosphatase activity
GO:0031490 chromatin DNA binding
GO:0033681 ATP-dependent 3'-5' DNA/RNA helicase activity
GO:0034459 ATP-dependent 3'-5' RNA helicase activity
GO:0035197 siRNA binding
GO:0035613 RNA stem-loop binding
GO:0043140 ATP-dependent 3'-5' DNA helicase activity
GO:0045142 triplex DNA binding
GO:0046872 metal ion binding
GO:0047429 nucleoside-triphosphate diphosphatase activity
GO:0061676 importin-alpha family protein binding
GO:0070063 RNA polymerase binding
GO:1905172 RISC complex binding
GO:1905538 polysome binding
GO:1990518 single-stranded DNA-dependent ATP-dependent 3'-5' DNA helicase activity
GO:1990825 sequence-specific mRNA binding
GO:1990841 promoter-specific chromatin binding

Biological Process:
GO:0000380 alternative mRNA splicing, via spliceosome
GO:0000398 mRNA splicing, via spliceosome
GO:0001649 osteoblast differentiation
GO:0002376 immune system process
GO:0006260 DNA replication
GO:0006351 transcription, DNA-templated
GO:0006353 DNA-templated transcription, termination
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006396 RNA processing
GO:0006397 mRNA processing
GO:0006417 regulation of translation
GO:0006954 inflammatory response
GO:0008380 RNA splicing
GO:0010501 RNA secondary structure unwinding
GO:0030423 targeting of mRNA for destruction involved in RNA interference
GO:0031047 gene silencing by RNA
GO:0032481 positive regulation of type I interferon production
GO:0032508 DNA duplex unwinding
GO:0032741 positive regulation of interleukin-18 production
GO:0035549 positive regulation of interferon-beta secretion
GO:0039695 DNA-templated viral transcription
GO:0044806 G-quadruplex DNA unwinding
GO:0045087 innate immune response
GO:0045089 positive regulation of innate immune response
GO:0045739 positive regulation of DNA repair
GO:0045740 positive regulation of DNA replication
GO:0045944 positive regulation of transcription from RNA polymerase II promoter
GO:0046833 positive regulation of RNA export from nucleus
GO:0048146 positive regulation of fibroblast proliferation
GO:0048511 rhythmic process
GO:0050434 positive regulation of viral transcription
GO:0050684 regulation of mRNA processing
GO:0050691 regulation of defense response to virus by host
GO:0050729 positive regulation of inflammatory response
GO:0051028 mRNA transport
GO:0051092 positive regulation of NF-kappaB transcription factor activity
GO:0060760 positive regulation of response to cytokine stimulus
GO:0070269 pyroptosis
GO:0070922 small RNA loading onto RISC
GO:0070934 CRD-mediated mRNA stabilization
GO:0071356 cellular response to tumor necrosis factor
GO:0071360 cellular response to exogenous dsRNA
GO:1902741 positive regulation of interferon-alpha secretion
GO:1903608 protein localization to cytoplasmic stress granule
GO:1904469 positive regulation of tumor necrosis factor secretion
GO:1904973 positive regulation of viral translation
GO:1905698 positive regulation of polysome binding
GO:2000373 positive regulation of DNA topoisomerase (ATP-hydrolyzing) activity
GO:2000637 positive regulation of gene silencing by miRNA
GO:2000765 regulation of cytoplasmic translation
GO:2000767 positive regulation of cytoplasmic translation
GO:2000778 positive regulation of interleukin-6 secretion

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005726 perichromatin fibrils
GO:0005730 nucleolus
GO:0005737 cytoplasm
GO:0005813 centrosome
GO:0005815 microtubule organizing center
GO:0005829 cytosol
GO:0005844 polysome
GO:0005856 cytoskeleton
GO:0015629 actin cytoskeleton
GO:0016020 membrane
GO:0016604 nuclear body
GO:0032991 macromolecular complex
GO:0035068 micro-ribonucleoprotein complex
GO:0036464 cytoplasmic ribonucleoprotein granule
GO:0042788 polysomal ribosome
GO:0070578 RISC-loading complex
GO:0070937 CRD-mediated mRNA stability complex
GO:0097165 nuclear stress granule
GO:1990904 ribonucleoprotein complex

-  Descriptions from all associated GenBank mRNAs
  LP895158 - Sequence 22 from Patent EP3253886.
AK226102 - Homo sapiens mRNA for ATP-dependent RNA helicase A variant, clone: ha01943.
BC137136 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone MGC:168756 IMAGE:9021133), complete cds.
BC144494 - Homo sapiens cDNA clone IMAGE:9053021.
L13848 - Human RNA helicase A mRNA, complete cds.
AB515351 - Synthetic construct DNA, clone: pF1KE1056, Homo sapiens DHX9 gene for DEAH (Asp-Glu-Ala-His) box polypeptide 9, without stop codon, in Flexi system.
Y10658 - H.sapiens mRNA for nuclear DNA helicase II.
AK310364 - Homo sapiens cDNA, FLJ17406.
AK308165 - Homo sapiens cDNA, FLJ98113.
BC014246 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:4642858), partial cds.
AF086352 - Homo sapiens full length insert cDNA clone ZD63A08.
BC025245 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:5021788), partial cds.
BC008773 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:3140089), partial cds.
JD050394 - Sequence 31418 from Patent EP1572962.
JD226940 - Sequence 207964 from Patent EP1572962.
AK096582 - Homo sapiens cDNA FLJ39263 fis, clone OCBBF2009571, highly similar to ATP-dependent RNA helicase A (EC 3.6.1.-).
BC032742 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:5575918), partial cds.
BC107881 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:6495148), partial cds.
BC058896 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:6501532), partial cds.
JD113853 - Sequence 94877 from Patent EP1572962.
U03643 - Human leukophysin (LKP) mRNA, complete cds.
JD272604 - Sequence 253628 from Patent EP1572962.
JD127370 - Sequence 108394 from Patent EP1572962.
JD552916 - Sequence 533940 from Patent EP1572962.
JD538669 - Sequence 519693 from Patent EP1572962.
BC071950 - Homo sapiens DEAH (Asp-Glu-Ala-His) box polypeptide 9, mRNA (cDNA clone IMAGE:6648154), partial cds.
JD042881 - Sequence 23905 from Patent EP1572962.
AK130564 - Homo sapiens cDNA FLJ27054 fis, clone SPL00538, highly similar to ATP-dependent RNA helicase A.
JD274278 - Sequence 255302 from Patent EP1572962.
JD183233 - Sequence 164257 from Patent EP1572962.
JD438597 - Sequence 419621 from Patent EP1572962.
AB451372 - Homo sapiens DHX9 mRNA for ATP-dependent RNA helicase A, partial cds, clone: FLJ08056AAAF.
AB451248 - Homo sapiens DHX9 mRNA for ATP-dependent RNA helicase A, complete cds, clone: FLJ08056AAAN.
JD490758 - Sequence 471782 from Patent EP1572962.
JD459337 - Sequence 440361 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q08211 (Reactome details) participates in the following event(s):

R-HSA-72107 Formation of the Spliceosomal E complex
R-HSA-3134954 DHX9 binds DNA
R-HSA-72143 Lariat Formation and 5'-Splice Site Cleavage
R-HSA-72139 Formation of the active Spliceosomal C (B*) complex
R-HSA-72124 Formation of the Spliceosomal A Complex
R-HSA-72127 Formation of the Spliceosomal B Complex
R-HSA-72130 Formation of an intermediate Spliceosomal C (Bact) complex
R-HSA-156661 Formation of Exon Junction Complex
R-HSA-3134953 DHX36 or DHX9 binds MyD88
R-HSA-72163 mRNA Splicing - Major Pathway
R-HSA-3134963 DEx/H-box helicases activate type I IFN and inflammatory cytokines production
R-HSA-72172 mRNA Splicing
R-HSA-1834949 Cytosolic sensors of pathogen-associated DNA
R-HSA-72203 Processing of Capped Intron-Containing Pre-mRNA
R-HSA-168249 Innate Immune System
R-HSA-8953854 Metabolism of RNA
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: B2RNV4, DDX9, DHX9_HUMAN, LKP, NDH2, NM_001357, NP_001348, Q05CI5, Q08211, Q12803, Q32Q22, Q5VY62, Q6PD69, Q99556
UCSC ID: uc001gpr.3
RefSeq Accession: NM_001357
Protein: Q08211 (aka DHX9_HUMAN)
CCDS: CCDS41444.1

-  Gene Model Information
category: coding nonsense-mediated-decay: no RNA accession: NM_001357.4
exon count: 28CDS single in 3' UTR: no RNA size: 4543
ORF size: 3813CDS single in intron: no Alignment % ID: 99.98
txCdsPredict score: 7779.50frame shift in genome: no % Coverage: 99.85
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: yes # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.