Human Gene DHX9 (ENST00000367549.4) from GENCODE V44
Description: Homo sapiens DExH-box helicase 9 (DHX9), transcript variant 2, non-coding RNA. (from RefSeq NR_033302) 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]. Gencode Transcript: ENST00000367549.4 Gencode Gene: ENSG00000135829.17 Transcript (Including UTRs) Position: hg38 chr1:182,839,347-182,887,982 Size: 48,636 Total Exon Count: 28 Strand: + Coding Region Position: hg38 chr1:182,842,567-182,887,434 Size: 44,868 Coding Exon Count: 27
ID:DHX9_HUMAN DESCRIPTION: RecName: Full=ATP-dependent RNA helicase A; Short=RHA; EC=3.6.4.13; 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.
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.
ModBase Predicted Comparative 3D Structure on Q08211
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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.
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
LP895158 - Sequence 22 from Patent EP3253886. AK226102 - Homo sapiens mRNA for ATP-dependent RNA helicase A variant, clone: ha01943. AK308165 - Homo sapiens cDNA, FLJ98113. 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. 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. 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. 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.
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
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