Dhx9 DExH-box helicase 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Dhx9provided by RGD
Official Full Name: DExH-box helicase 9provided by RGD
Primary source: RGD:1308548
See related: Ensembl:ENSRNOG00000002735 AllianceGenome:RGD:1308548
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Predicted to enable several functions, including helicase activity; nucleic acid binding activity; and ribonucleoprotein complex binding activity. Predicted to be involved in several processes, including DNA geometric change; regulation of defense response; and regulation of gene expression. Predicted to act upstream of or within cellular response to heat and circadian rhythm. Predicted to be located in several cellular components, including cytoskeleton; nuclear lumen; and ribonucleoprotein granule. Predicted to be part of several cellular components, including CRD-mediated mRNA stability complex; RISC complex; and RISC-loading complex. Predicted to be active in cytoplasm and nucleolus. Orthologous to human DHX9 (DExH-box helicase 9). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Spleen (RPKM 219.5), Thymus (RPKM 203.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 13q21

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	13	NC_086031.1 (68152813..68189580, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	13	NC_051348.1 (65602322..65639098, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	13	NC_005112.4 (70885503..70922278, complement)

Chromosome 13 - NC_086031.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

AA875461 (e-PCR)
- UniSTS:245846

RH143807 (e-PCR)
- UniSTS:233053

Gene Ontology Provided by RGD

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/RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables 3'-5' RNA helicase activity	ISO Inferred from Sequence Orthology 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 DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables DNA replication origin binding	ISO Inferred from Sequence Orthology more info
enables RISC complex binding	ISO Inferred from Sequence Orthology 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 helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	ISO Inferred from Sequence Orthology 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 stem-loop binding	ISO Inferred from Sequence Orthology more info
enables chromatin DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables double-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables importin-alpha family protein binding	ISO Inferred from Sequence Orthology more info
enables mRNA binding	ISO Inferred from Sequence Orthology more info
enables nucleoside triphosphate diphosphatase activity	ISO Inferred from Sequence Orthology more info
enables promoter-specific chromatin binding	ISO Inferred from Sequence Orthology more info
enables regulatory region RNA binding	ISO Inferred from Sequence Orthology 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 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 DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables transcription coactivator activity	ISO Inferred from Sequence Orthology more info
enables transcription coregulator activity	ISO Inferred from Sequence Orthology more info
enables triplex DNA binding	ISO Inferred from Sequence Orthology 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-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 RISC complex assembly	ISO Inferred from Sequence Orthology more info
involved_in RNA secondary structure unwinding	ISO Inferred from Sequence Orthology more info
involved_in alternative mRNA splicing, via spliceosome	ISO Inferred from Sequence Orthology more info
involved_in biological_process	ND No biological Data available more info
involved_in cellular response to exogenous dsRNA	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within cellular response to heat	ISO Inferred from Sequence Orthology more info
involved_in cellular response to tumor necrosis factor	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in miRNA-mediated post-transcriptional gene silencing	ISO Inferred from Sequence Orthology 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 replication	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of RNA export from nucleus	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of cytoplasmic translation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of fibroblast proliferation	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of innate immune response	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-alpha production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interferon-beta production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-18 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of interleukin-6 production	ISO Inferred from Sequence Orthology more info
involved_in positive regulation of response to cytokine stimulus	ISO Inferred from Sequence Orthology 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 tumor necrosis factor production	ISO Inferred from Sequence Orthology 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 protein-containing complex assembly	ISO Inferred from Sequence Orthology more info
involved_in pyroptosis	ISO Inferred from Sequence Orthology more info
involved_in regulation of cytoplasmic translation	ISO Inferred from Sequence Orthology more info
involved_in regulation of defense response to virus by host	ISO Inferred from Sequence Orthology more info
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 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 RISC complex	ISO Inferred from Sequence Orthology more info
part_of RISC-loading complex	ISO Inferred from Sequence Orthology more info
located_in actin cytoskeleton	ISO Inferred from Sequence Orthology more info
located_in centrosome	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasmic ribonucleoprotein granule	ISO Inferred from Sequence Orthology more info
located_in cytosol	ISO Inferred from Sequence Orthology more info
is_active_in intracellular anatomical structure	IBA Inferred from Biological aspect of Ancestor more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nuclear stress granule	ISO Inferred from Sequence Orthology more info
is_active_in nucleolus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleolus	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in perichromatin fibrils	ISO Inferred from Sequence Orthology 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

General protein information

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Preferred Names: ATP-dependent RNA helicase A

Names: DEAH (Asp-Glu-Ala-His) box helicase 9; DEAH (Asp-Glu-Ala-His) box polypeptide 9; DEAH-box helicase 9

NP_001382485.1

EC 3.6.1.-

XP_006250058.1

EC 3.6.1.-

XP_008767855.1

EC 3.6.1.-

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_001395556.1 → NP_001382485.1 ATP-dependent RNA helicase A

Status: VALIDATED

Source sequence(s)

JAXUCZ010000013

UniProtKB/TrEMBL

A0A8I6ABZ7, A6ICV0, D4A9D6

Related

ENSRNOP00000090956.1, ENSRNOT00000116976.1

Conserved Domains (4) summary

COG1643
Location:337 → 1055

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

cd17972
Location:333 → 566

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

cd19854
Location:3 → 71

DSRM_DHX9_rpt1; first double-stranded RNA binding motif of DEAH box protein 9 (DHX9) and similar proteins

cd19855
Location:181 → 255

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

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

Reference GRCr8

Genomic

NC_086031.1 Reference GRCr8

Range

68152813..68189580 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006249996.5 → XP_006250058.1 ATP-dependent RNA helicase A isoform X1

UniProtKB/TrEMBL

A6ICV0, D4A9D6

Conserved Domains (6) summary

smart00358
Location:5 → 69

DSRM; Double-stranded RNA binding motif

smart00487
Location:384 → 571

DEXDc; DEAD-like helicases superfamily

smart00847
Location:840 → 921

HA2; Helicase associated domain (HA2) Add an annotation

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
XM_008769633.3 → XP_008767855.1 ATP-dependent RNA helicase A isoform X2

UniProtKB/TrEMBL

A6ICV0, D4A9D6

Conserved Domains (5) summary

smart00487
Location:168 → 355

DEXDc; DEAD-like helicases superfamily

smart00847
Location:624 → 705

HA2; Helicase associated domain (HA2) Add an annotation

cd00046
Location:191 → 332

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:421 → 554

Helicase_C; Helicase conserved C-terminal domain

pfam07717
Location:745 → 859

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

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001107184.1: Suppressed sequence

Description

NM_001107184.1: This RefSeq was removed because currently there is insufficient support for the transcript and the protein.