Dhx9 DExH-box helicase 9 [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Dhx9provided by MGI
Official Full Name: DExH-box helicase 9provided by MGI
Primary source: MGI:MGI:108177
See related: Ensembl:ENSMUSG00000042699 AllianceGenome:MGI:108177
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Mus musculus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Mus; Mus
Also known as: RHA; Ddx9; HEL-5; NDHII; mHEL-5
Summary: Enables regulatory region RNA binding activity. Involved in positive regulation of interleukin-18 production; pyroptotic inflammatory response; and regulation of defense response. Acts upstream of or within cellular response to heat and circadian rhythm. Located in nucleolus. Is expressed in several structures, including alimentary system; central nervous system; lung; salivary gland primordium; and sensory organ. Orthologous to human DHX9 (DExH-box helicase 9). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Broad expression in CNS E11.5 (RPKM 71.6), CNS E14 (RPKM 55.5) and 21 other tissues See more
Orthologs: human all
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Genomic context

Location:: 1 G3; 1 65.37 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	1	NC_000067.7 (153331506..153363464, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	1	NC_000067.6 (153455756..153487688, complement)

Chromosome 1 - NC_000067.7 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

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Expression

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See details

Project title: Mouse ENCODE transcriptome data
Description: RNA profiling data sets generated by the Mouse ENCODE project.
BioProject: PRJNA66167
Publication: PMID 25409824
Analysis date: n/a

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells.
Title: DHX9 maintains epithelial homeostasis by restraining R-loop-mediated genomic instability in intestinal stem cells.
PARP1, DIDO3, and DHX9 Proteins Mutually Interact in Mouse Fibroblasts, with Effects on DNA Replication Dynamics, Senescence, and Oncogenic Transformation.
Title: PARP1, DIDO3, and DHX9 Proteins Mutually Interact in Mouse Fibroblasts, with Effects on DNA Replication Dynamics, Senescence, and Oncogenic Transformation.
DHX9 Strengthens Atherosclerosis Progression By Promoting Inflammation in Macrophages.
Title: DHX9 Strengthens Atherosclerosis Progression By Promoting Inflammation in Macrophages.
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.
Nucleic DHX9 cooperates with STAT1 to transcribe interferon-stimulated genes.
Title: Nucleic DHX9 cooperates with STAT1 to transcribe interferon-stimulated genes.
Cytosolic Nuclear Sensor Dhx9 Controls Medullary Thymic Epithelial Cell Differentiation by p53-Mediated Pathways.
Title: Cytosolic Nuclear Sensor Dhx9 Controls Medullary Thymic Epithelial Cell Differentiation by p53-Mediated Pathways.
DHX9/YB-1 complex induced alternative splicing of Kruppel-like factor 5 mRNA is involved in phenotypic transformation of vascular smooth muscle cells obtained from mouse model of aortic dissection.
Title: Involvement of DHX9/YB-1 complex induced alternative splicing of Krüppel-like factor 5 mRNA in phenotypic transformation of vascular smooth muscle cells.
A DNA-sensing-independent role of a nuclear RNA helicase, DHX9, has been demonstrated in stimulation of NF-kappaB-mediated innate immunity against DNA virus infection.
Title: A DNA-sensing-independent role of a nuclear RNA helicase, DHX9, in stimulation of NF-κB-mediated innate immunity against DNA virus infection.
our study supports the presence of a p53-independent mechanism of cell death and cell cycle arrest resulting from DHX9 inhibition. our results support the feasibility of targeting DHX9 as a chemotherapeutic approach in p53-deficient tumors.
Title: Dependence of p53-deficient cells on the DHX9 DExH-box helicase.

Submit: New GeneRIF Correction See all GeneRIFs (11)

Variation

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Alleles

Alleles of this type are documented at Mouse Genome Informatics (MGI)

Endonuclease-mediated (4) 1 citation
Targeted (4) 1 citation
Transposon induced (1) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Dhx9 (e-PCR), detects polymorphism
- UniSTS:479098

PMC24884P1 (e-PCR)
- UniSTS:272276

AI326842 (e-PCR)
- UniSTS:165110

Gene Ontology Provided by MGI

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	ISO Inferred from Sequence Orthology more info
enables 3'-5' DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 3'-5' DNA/RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables 3'-5' DNA/RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 3'-5' RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables 3'-5' RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	IBA Inferred from Biological aspect of Ancestor more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent H2AZ histone chaperone activity	IEA Inferred from Electronic Annotation more info
enables ATP-dependent H3-H4 histone complex chaperone activity	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables DNA clamp loader activity	IEA Inferred from Electronic Annotation more info
enables DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables DNA replication origin binding	ISO Inferred from Sequence Orthology more info
enables DNA replication origin binding	ISS Inferred from Sequence or Structural Similarity more info
enables RISC complex binding	ISO Inferred from Sequence Orthology more info
enables RISC complex binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA polymerase II complex binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II-specific DNA-binding transcription factor binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase binding	ISO Inferred from Sequence Orthology more info
enables RNA polymerase binding	ISS Inferred from Sequence or Structural Similarity more info
enables RNA stem-loop binding	ISO Inferred from Sequence Orthology more info
enables RNA stem-loop binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables chromatin extrusion motor activity	IEA Inferred from Electronic Annotation more info
enables cohesin loader activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables importin-alpha family protein binding	ISO Inferred from Sequence Orthology more info
enables importin-alpha family protein binding	ISS Inferred from Sequence or Structural Similarity more info
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables nucleoside triphosphate diphosphatase activity	ISO Inferred from Sequence Orthology more info
enables nucleoside triphosphate diphosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISS Inferred from Sequence or Structural Similarity more info
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 regulatory region RNA binding	ISO Inferred from Sequence Orthology more info
enables ribonucleoside triphosphate phosphatase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ribosome binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific mRNA binding	ISO Inferred from Sequence Orthology more info
enables sequence-specific mRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables siRNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded 3'-5' DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables single-stranded 3'-5' DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISS Inferred from Sequence or Structural Similarity more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info
enables triplex DNA binding	ISO Inferred from Sequence Orthology more info
enables triplex DNA binding	ISS Inferred from Sequence or Structural Similarity more info

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

Component	Evidence Code	Pubs
part_of CRD-mediated mRNA stability complex	ISO Inferred from Sequence Orthology more info
part_of CRD-mediated mRNA stability complex	ISS Inferred from Sequence or Structural Similarity more info
part_of RISC complex	ISO Inferred from Sequence Orthology more info
part_of RISC complex	ISS Inferred from Sequence or Structural Similarity more info
part_of RISC-loading complex	ISO Inferred from Sequence Orthology more info
part_of RISC-loading complex	ISS Inferred from Sequence or Structural Similarity more info
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in actin cytoskeleton	ISS Inferred from Sequence or Structural Similarity more info
located_in centrosome	IEA Inferred from Electronic Annotation more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic ribonucleoprotein granule	ISS Inferred from Sequence or Structural Similarity more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear body	ISS Inferred from Sequence or Structural Similarity more info
located_in nuclear stress granule	ISO Inferred from Sequence Orthology more info
located_in nuclear stress granule	ISS Inferred from Sequence or Structural Similarity more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	IDA Inferred from Direct Assay more info	PubMed
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perichromatin fibrils	ISO Inferred from Sequence Orthology more info
located_in perichromatin fibrils	ISS Inferred from Sequence or Structural Similarity more info
part_of protein-containing complex	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info	PubMed
part_of ribonucleoprotein complex	ISS Inferred from Sequence or Structural Similarity more info

General protein information

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Preferred Names: ATP-dependent RNA helicase A

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

NP_001392438.1

EC 3.6.4.13

NP_031868.2

EC 3.6.4.13

XP_030102263.1

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.

mRNA and Protein(s)

NM_001405509.1 → NP_001392438.1 ATP-dependent RNA helicase A isoform 1

Status: VALIDATED

Source sequence(s)

AC098709, AC099712

UniProtKB/TrEMBL

E9QNN1

Related

ENSMUSP00000038135.6, ENSMUST00000042141.12
NM_007842.3 → NP_031868.2 ATP-dependent RNA helicase A isoform 2

Status: VALIDATED

Source sequence(s)

AC098709, AC099712

Consensus CDS

CCDS78706.1

UniProtKB/Swiss-Prot

O35931, O54703, O70133, Q5FWY1, Q6R5F7, Q9CSA2

UniProtKB/TrEMBL

A0A087WPL5

Related

ENSMUSP00000139825.2, ENSMUST00000186380.7

Conserved Domains (6) summary

smart00358
Location:5 → 69

DSRM; Double-stranded RNA binding motif

smart00847
Location:840 → 921

HA2; Helicase associated domain (HA2) Add an annotation

COG1643
Location:336 → 1054

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

cd00046
Location:407 → 548

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.

pfam00271
Location:637 → 770

Helicase_C; Helicase conserved C-terminal domain

pfam07717
Location:961 → 1075

OB_NTP_bind; Oligonucleotide/oligosaccharide-binding (OB)-fold

RNA

NR_175951.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC098709, AC099712
NR_175952.1 RNA Sequence

Status: VALIDATED

Source sequence(s)

AC098709, AC099712

RefSeqs of Annotated Genomes: GCF_000001635.27-RS_2024_02

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

Reference GRCm39 C57BL/6J

Genomic

NC_000067.7 Reference GRCm39 C57BL/6J

Range

153331506..153363464 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_030246403.2 → XP_030102263.1 ATP-dependent RNA helicase A isoform X2

UniProtKB/Swiss-Prot

O35931, O54703, O70133, Q5FWY1, Q6R5F7, Q9CSA2

Conserved Domains (3) summary

COG1643
Location:120 → 838

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

cd17972
Location:116 → 349

DEXHc_DHX9; DEXH-box helicase domain of DEAH-box helicase 9

cd19855
Location:1 → 38

DSRM_DHX9_rpt2; second double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins