Scn9a sodium voltage-gated channel alpha subunit 9 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scn9aprovided by RGD
Official Full Name: sodium voltage-gated channel alpha subunit 9provided by RGD
Primary source: RGD:69368
See related: EnsemblRapid:ENSRNOG00000006639 AllianceGenome:RGD:69368
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
Also known as: PN1; Scn2a; Nav1.7
Summary: Predicted to enable voltage-gated sodium channel activity. Involved in behavioral response to formalin induced pain and negative regulation of action potential. Located in axon. Human ortholog(s) of this gene implicated in erythromelalgia and paroxysmal extreme pain disorder. Orthologous to human SCN9A (sodium voltage-gated channel alpha subunit 9). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 67.9), Adrenal (RPKM 18.0) and 3 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 3q21

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (71553185..71701377, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (51145148..51293342, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (52583953..52664209, complement)

Chromosome 3 - NC_086021.1 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 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?

Long noncoding RNA small nucleolar RNA host gene 5 facilitates neuropathic pain in spinal nerve injury by promoting SCN9A expression via CDK9.
Title: Long noncoding RNA small nucleolar RNA host gene 5 facilitates neuropathic pain in spinal nerve injury by promoting SCN9A expression via CDK9.
Correlative increasing expressions of KIF5b and Nav1.7 in DRG neurons of rats under neuropathic pain conditions.
Title: Correlative increasing expressions of KIF5b and Nav1.7 in DRG neurons of rats under neuropathic pain conditions.
Extracellular signal-regulated kinase phosphorylation enhancement and NaV1.7 sodium channel upregulation in rat dorsal root ganglia neurons contribute to resiniferatoxin-induced neuropathic pain: The efficacy and mechanism of pulsed radiofrequency therapy.
Title: Extracellular signal-regulated kinase phosphorylation enhancement and Na(V)1.7 sodium channel upregulation in rat dorsal root ganglia neurons contribute to resiniferatoxin-induced neuropathic pain: The efficacy and mechanism of pulsed radiofrequency therapy.
NGF-Induced Nav1.7 Upregulation Contributes to Chronic Post-surgical Pain by Activating SGK1-Dependent Nedd4-2 Phosphorylation.
Title: NGF-Induced Nav1.7 Upregulation Contributes to Chronic Post-surgical Pain by Activating SGK1-Dependent Nedd4-2 Phosphorylation.
Involvement of the Sodium Channel Nav1.7 in Paclitaxel-induced Peripheral Neuropathy through ERK1/2 Signaling in Rats.
Title: Involvement of the Sodium Channel Nav1.7 in Paclitaxel-induced Peripheral Neuropathy through ERK1/2 Signaling in Rats.
Dorsal root ganglion neurons expressing the CRMP2-K374A mutant also exhibited total sodium current increases after exposure to TNF-alpha, indicating that these effects were independent of SUMOylation of CRMP2.
Title: TNF-α mediated upregulation of Na(V)1.7 currents in rat dorsal root ganglion neurons is independent of CRMP2 SUMOylation.
enhancement of NaV1.7 vesicular trafficking and surface delivery under conditions that mimic a disease state provides new insights into the contribution of NaV1.7 to inflammatory pain.
Title: Building sensory axons: Delivery and distribution of Na(V)1.7 channels and effects of inflammatory mediators.
Nav1.7 was closely related to neuropathic pain induced by nerve injury.
Title: Voltage-gated sodium channel 1.7 expression decreases in dorsal root ganglia in a spinal nerve ligation neuropathic pain model.
miR-182 can alleviate SNI- induced neuropathic pain through regulating Nav1.7 in rats
Title: MicroRNA-182 Alleviates Neuropathic Pain by Regulating Nav1.7 Following Spared Nerve Injury in Rats.
In this study, with the established link to inflammatory pain, we found that Nav1.7 and ERK both play important roles in the induction of inflammatory pain caused by pulpitis. We also found a correlation between the expression levels of Nav1.7 and ERK and the degree of inflammatory pain.
Title: Nav1.7 via Promotion of ERK in the Trigeminal Ganglion Plays an Important Role in the Induction of Pulpitis Inflammatory Pain.

Submit: New GeneRIF Correction See all GeneRIFs (40)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Scn3a (e-PCR), detects polymorphism
- UniSTS:516640

RH138415 (e-PCR)
- UniSTS:220502

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in action potential propagation	IEA Inferred from Electronic Annotation more info
involved_in action potential propagation	ISO Inferred from Sequence Orthology more info
involved_in action potential propagation	ISS Inferred from Sequence or Structural Similarity more info
involved_in behavioral response to formalin induced pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavioral response to pain	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within behavioral response to pain	ISO Inferred from Sequence Orthology more info
involved_in behavioral response to pain	ISO Inferred from Sequence Orthology more info
involved_in circadian rhythm	IEA Inferred from Electronic Annotation more info
involved_in circadian rhythm	ISO Inferred from Sequence Orthology more info
involved_in detection of mechanical stimulus involved in sensory perception	IEA Inferred from Electronic Annotation more info
involved_in detection of mechanical stimulus involved in sensory perception	ISO Inferred from Sequence Orthology more info
involved_in detection of temperature stimulus involved in sensory perception of pain	IEA Inferred from Electronic Annotation more info
involved_in detection of temperature stimulus involved in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within inflammatory response	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in neuronal action potential	IEA Inferred from Electronic Annotation more info
involved_in neuronal action potential	ISO Inferred from Sequence Orthology more info
involved_in post-embryonic development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within post-embryonic development	ISO Inferred from Sequence Orthology more info
involved_in response to toxic substance	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within response to toxic substance	ISO Inferred from Sequence Orthology more info
involved_in rhythmic excitation	NAS Non-traceable Author Statement more info	PubMed
involved_in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in sensory perception of pain	ISS Inferred from Sequence or Structural Similarity more info
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon terminus	IEA Inferred from Electronic Annotation more info
located_in axon terminus	ISO Inferred from Sequence Orthology more info
located_in axon terminus	ISS Inferred from Sequence or Structural Similarity more info
located_in node of Ranvier	IEA Inferred from Electronic Annotation more info
located_in node of Ranvier	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
part_of voltage-gated sodium channel complex	IBA Inferred from Biological aspect of Ancestor more info
part_of voltage-gated sodium channel complex	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: sodium channel protein type 9 subunit alpha

Names: peripheral sodium channel 1; sodium channel protein type IX subunit alpha; sodium channel, voltage-gated, type 9, alpha polypeptide; sodium channel, voltage-gated, type IX, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.7

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_133289.2 → NP_579823.1 sodium channel protein type 9 subunit alpha

See identical proteins and their annotated locations for NP_579823.1

Status: VALIDATED

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

O08562

UniProtKB/TrEMBL

A0A8L2QSN0

Related

ENSRNOP00000059170.2, ENSRNOT00000065126.5

Conserved Domains (6) summary

smart00015
Location:1886 → 1908

IQ; Calmodulin-binding motif

cd13433
Location:1456 → 1508

Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits

pfam00520
Location:1224 → 1464

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1185

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:487 → 606

Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel

pfam16905
Location:1780 → 1835

GPHH; Voltage-dependent L-type calcium channel, IQ-associated

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_086021.1 Reference GRCr8

Range

71553185..71701377 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063284600.1 → XP_063140670.1 sodium channel protein type 9 subunit alpha isoform X2
XM_063284599.1 → XP_063140669.1 sodium channel protein type 9 subunit alpha isoform X1