Scn9a sodium channel, voltage-gated, type IX, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn9aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type IX, alphaprovided by MGI
Primary source: MGI:MGI:107636
See related: Ensembl:ENSMUSG00000075316 AllianceGenome:MGI:107636
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: PN1; Nav1.7; mKIAA4197
Summary: Predicted to enable sodium ion binding activity and voltage-gated sodium channel activity. Involved in behavioral response to pain; circadian rhythm; and detection of stimulus involved in sensory perception. Acts upstream of or within inflammatory response; post-embryonic development; and response to toxic substance. Predicted to be located in axon terminus and plasma membrane. Predicted to be part of voltage-gated sodium channel complex. Predicted to be active in axon. Is expressed in several structures, including brain; gut; immune system; male reproductive gland or organ; and respiratory system epithelium. 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, Dec 2024]
Expression: Biased expression in CNS E18 (RPKM 4.9), whole brain E14.5 (RPKM 3.0) and 6 other tissues See more
Orthologs: human all
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Genomic context

Location:: 2 C1.3; 2 39.13 cM

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	2	NC_000068.8 (66310424..66465456, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (66480080..66635114, complement)

Chromosome 2 - NC_000068.8 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

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?

The voltage-gated sodium channel NaV1.7 underlies endometriosis-associated chronic pelvic pain.
Title: The voltage-gated sodium channel Na(V)1.7 underlies endometriosis-associated chronic pelvic pain.
Nav1.7 is essential for nociceptor action potentials in the mouse in a manner independent of endogenous opioids.
Title: Nav1.7 is essential for nociceptor action potentials in the mouse in a manner independent of endogenous opioids.
Nav1.7 gain-of-function mutation I228M triggers age-dependent nociceptive insensitivity and C-LTMR dysregulation.
Title: Na(v)1.7 gain-of-function mutation I228M triggers age-dependent nociceptive insensitivity and C-LTMR dysregulation.
Nav1.7 is required for normal C-low threshold mechanoreceptor function in humans and mice.
Title: Nav1.7 is required for normal C-low threshold mechanoreceptor function in humans and mice.
Selective optogenetic activation of NaV1.7-expressing afferents in NaV1.7-ChR2 mice induces nocifensive behavior without affecting responses to mechanical and thermal stimuli.
Title: Selective optogenetic activation of NaV1.7-expressing afferents in NaV1.7-ChR2 mice induces nocifensive behavior without affecting responses to mechanical and thermal stimuli.
Examination of the contribution of Nav1.7 to axonal propagation in nociceptors.
Title: Examination of the contribution of Nav1.7 to axonal propagation in nociceptors.
Two independent mouse lines carrying the Nav1.7 I228M gain-of-function variant display dorsal root ganglion neuron hyperexcitability but a minimal pain phenotype.
Title: Two independent mouse lines carrying the Nav1.7 I228M gain-of-function variant display dorsal root ganglion neuron hyperexcitability but a minimal pain phenotype.
Nav1.7 and MGO-mediated activation of TRPA1 play key roles in itch and hypoalgesia in a murine model of type 1 diabetes.
Title: The role of Na(v)1.7 and methylglyoxal-mediated activation of TRPA1 in itch and hypoalgesia in a murine model of type 1 diabetes.
data illustrated the therapeutic potential for 3'-O-methylorobol for histamine-dependent itching, and the small molecule inhibition of Nav1.7 may represent a useful strategy to develop novel therapeutics for itching.
Title: 3'-O-Methylorobol Inhibits the Voltage-Gated Sodium Channel Nav1.7 with Anti-Itch Efficacy in A Histamine-Dependent Itch Mouse Model.
This study demonstrated that nav1.7 contribution to peripheral nerves pain.
Title: NaV1.7 and pain: contribution of peripheral nerves.

Submit: New GeneRIF Correction See all GeneRIFs (28)

Variation

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Alleles

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

Endonuclease-mediated (5) 1 citation
Targeted (6) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Scn9a (e-PCR), detects polymorphism
- UniSTS:495997

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium channel activity	TAS Traceable Author Statement more info
enables sodium ion binding	ISO Inferred from Sequence Orthology more info
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor 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	ISS Inferred from Sequence or Structural Similarity more info
involved_in behavioral response to formalin induced pain	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within behavioral response to pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavioral response to pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in circadian rhythm	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in detection of mechanical stimulus involved in sensory perception	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in detection of temperature stimulus involved in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of action potential	ISO Inferred from Sequence Orthology more info
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
acts_upstream_of_or_within post-embryonic development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within response to toxic substance	IDA Inferred from Direct Assay 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
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
located_in axon	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 plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in plasma membrane	TAS Traceable Author Statement 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
part_of voltage-gated sodium channel complex	ISO Inferred from Sequence Orthology 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 25; sodium channel, voltage-gated, type IX, alpha polypeptide; voltage-gated sodium channel alpha subunit 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_001290674.1 → NP_001277603.1 sodium channel protein type 9 subunit alpha isoform a

See identical proteins and their annotated locations for NP_001277603.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (a).

Source sequence(s)

AK141871, AL928623, AL928726, BP765553

Consensus CDS

CCDS71063.1

UniProtKB/Swiss-Prot

A2ASI7, Q5DTI0, Q62205

UniProtKB/TrEMBL

B7ZWN0

Related

ENSMUSP00000097642.3, ENSMUST00000100064.9

Conserved Domains (5) summary

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
NM_001290675.1 → NP_001277604.1 sodium channel protein type 9 subunit alpha isoform b

See identical proteins and their annotated locations for NP_001277604.1

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks an in-frame exon but contains an alternate in-frame exon in the 5' coding region, and also contains an alternate in-frame splice site in the central coding region, compared to variant 1. The resulting isoform (b) is shorter than isoform a.

Source sequence(s)

AK141871, AL928623, AL928726, BP765553

UniProtKB/TrEMBL

B2RY06

Conserved Domains (5) summary

cd13433
Location:1445 → 1497

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

pfam00520
Location:1213 → 1453

Ion_trans; Ion transport protein

pfam06512
Location:970 → 1174

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:487 → 606

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

pfam16905
Location:1769 → 1824

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

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_000068.8 Reference GRCm39 C57BL/6J

Range

66310424..66465456 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499033.5 → XP_006499096.1 sodium channel protein type 9 subunit alpha isoform X1

UniProtKB/TrEMBL

B7ZWN0

Conserved Domains (5) summary

cd13433
Location:1456 → 1508

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

pfam00520
Location:1189 → 1464

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1185

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:488 → 693

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

pfam16905
Location:1780 → 1827

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006499035.5 → XP_006499098.1 sodium channel protein type 9 subunit alpha isoform X2

See identical proteins and their annotated locations for XP_006499098.1

UniProtKB/TrEMBL

B1AYL0, B2RY06

Related

ENSMUSP00000107973.2, ENSMUST00000112354.3

Conserved Domains (5) summary

cd13433
Location:1445 → 1497

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

pfam00520
Location:1178 → 1453

Ion_trans; Ion transport protein

pfam06512
Location:970 → 1174

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:488 → 682

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

pfam16905
Location:1769 → 1816

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

RNA

XR_001781564.3 RNA Sequence
XR_374432.5 RNA Sequence

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_018852.2: Suppressed sequence

Description

NM_018852.2: This RefSeq was permanently suppressed because currently there is insufficient support for the transcript and the protein.