Scn11a sodium channel, voltage-gated, type XI, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn11aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type XI, alphaprovided by MGI
Primary source: MGI:MGI:1345149
See related: Ensembl:ENSMUSG00000034115 AllianceGenome:MGI:1345149
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: NaN; NaT; NSS2; SNS2; NaV1.9
Summary: Enables voltage-gated sodium channel activity. Involved in several processes, including behavioral response to chemical pain; detection of stimulus involved in sensory perception of pain; and monoatomic cation transmembrane transport. Acts upstream of or within establishment of localization in cell and sodium ion transport. Located in C-fiber and plasma membrane. Is active in axonal growth cone and neuronal cell body. Is expressed in several structures, including alimentary system; central nervous system; immune system; reproductive system; and sensory organ. Used to study familial episodic pain syndrome 3 and hereditary sensory neuropathy. Human ortholog(s) of this gene implicated in familial episodic pain syndrome 3 and hereditary sensory and autonomic neuropathy type 7. Orthologous to human SCN11A (sodium voltage-gated channel alpha subunit 11). [provided by Alliance of Genome Resources, Dec 2024]
Expression: Low expression observed in reference dataset See more
Orthologs: human all
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Genomic context

Location:: 9 F3; 9 71.33 cM

Exon count:: 28

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCm39 (GCF_000001635.27)	9	NC_000075.7 (119582829..119654522, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	9	NC_000075.6 (119753763..119825456, complement)

Chromosome 9 - NC_000075.7 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: 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?

SCN11A gene deletion causes sensorineural hearing loss by impairing the ribbon synapses and auditory nerves.
Title: SCN11A gene deletion causes sensorineural hearing loss by impairing the ribbon synapses and auditory nerves.
Gain-of-function mutation in SCN11A causes itch and affects neurogenic inflammation and muscle function in Scn11a+/L799P mice.
Title: Gain-of-function mutation in SCN11A causes itch and affects neurogenic inflammation and muscle function in Scn11a+/L799P mice.
abnormal activation of Nav1.9 channels by Nitric Oxide (NO) is responsible for MOH induced by triptan migraine medicine. Deletion of the Scn11a gene in Medication-overuse headache mice abrogates NO-mediated symptoms, including cephalic and extracephalic allodynia, photophobia and phonophobia.
Title: Maladaptive activation of Nav1.9 channels by nitric oxide causes triptan-induced medication overuse headache.
crucial for shaping the action potential upstroke and keeping the NaV1.8 voltage threshold within reach
Title: Heat-resistant action potentials require TTX-resistant sodium channels Na(V)1.8 and Na(V)1.9.
data suggest an important contribution of NaV1.9 to itch signaling.
Title: A disease mutation reveals a role for NaV1.9 in acute itch.
Two missense var- iants, p.R222S and p.R222H of Nav1.9, were identified in SCN11A by linkage analysis and exome analy- sis
Title: [Paroxysmal limb intolerable pain (infantile pain episodes associated with novel Nav1.9 mutations in familial episodic pain syndrome)].
This study demonstrated that NaV1.9 presumably contributes to acute thermal and mechanical nociception in mice.
Title: Reduced excitability and impaired nociception in peripheral unmyelinated fibers from Nav1.9-null mice.
Recently Nav1.9, a voltage-gated sodium channel subtype, has been established as a genetic influence for certain peripheral pain syndromes.
Title: Infantile Pain Episodes Associated with Novel Nav1.9 Mutations in Familial Episodic Pain Syndrome in Japanese Families.
A missense mutation (p.V1184A) in NaV1.9 leads to cold-aggravated peripheral pain.
Title: Cold-aggravated pain in humans caused by a hyperactive NaV1.9 channel mutant.
We conclude that Nav1.9 acts as a subthreshold amplifier in cold-sensitive nociceptive neurons and is required for the perception of cold pain under normal and pathological conditions.
Title: The Nav1.9 channel is a key determinant of cold pain sensation and cold allodynia.

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 (9) 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

AF118044 (e-PCR)
- UniSTS:179993

Scn11a (e-PCR), detects polymorphism
- UniSTS:532893

Scn11a (e-PCR), detects polymorphism
- UniSTS:496050

Scn11a (e-PCR), detects polymorphism
- UniSTS:144374

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables voltage-gated sodium channel activity	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity	IMP Inferred from Mutant Phenotype more info	PubMed
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in G protein-coupled receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in action potential initiation	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in acute inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in artery development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in axonogenesis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavioral response to acetic acid induced pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in behavioral response to formalin induced 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 cAMP/PKA signal transduction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcitonin gene-related peptide receptor signaling pathway	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in calcium ion transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cell motility	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cellular response to cold	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chemosensory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in chronic inflammatory response	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 mechanical stimulus involved in sensory perception of pain	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 establishment of localization in cell	IDA Inferred from Direct Assay more info	PubMed
involved_in inflammatory response	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in mast cell degranulation	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 membrane depolarization during action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
involved_in micturition	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	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in reflex	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in regulation of membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to auditory stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to cold	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to cyclophosphamide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to heat	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to high light intensity	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to nitric oxide	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to prostaglandin E	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to toxic substance	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in response to xenobiotic stimulus	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of itch	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of pain	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in skeletal muscle organ development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in small intestine smooth muscle contraction	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in sodium ion transmembrane transport	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within sodium ion transport	IDA Inferred from Direct Assay more info	PubMed
involved_in thermosensory behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in thigmotaxis	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transmission of nerve impulse	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
located_in C-fiber	IDA Inferred from Direct Assay more info	PubMed
is_active_in axon	IBA Inferred from Biological aspect of Ancestor more info
is_active_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon	IDA Inferred from Direct Assay more info	PubMed
located_in axon	ISO Inferred from Sequence Orthology more info
is_active_in axonal growth cone	IDA Inferred from Direct Assay more info	PubMed
is_active_in cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in glutamatergic synapse	ISO Inferred from Sequence Orthology more info
is_active_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in neuronal cell body	IMP Inferred from Mutant Phenotype more info	PubMed
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	IMP Inferred from Mutant Phenotype more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic 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 11 subunit alpha

Names: sensory neuron sodium channel 2; sodium channel protein type XI subunit alpha; sodium channel, voltage-gated, type XI, alpha polypeptide; voltage-gated sodium channel NAV1.9b; voltage-gated sodium channel subunit alpha Nav1.9

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_011887.3 → NP_036017.3 sodium channel protein type 11 subunit alpha

See identical proteins and their annotated locations for NP_036017.3

Status: VALIDATED

Source sequence(s)

AC124662, AC162937

Consensus CDS

CCDS40804.1

UniProtKB/Swiss-Prot

E9QM88, Q9JMD4, Q9R053

UniProtKB/TrEMBL

A0A0R5RP39

Related

ENSMUSP00000065466.8, ENSMUST00000070617.8

Conserved Domains (3) summary

cd13433
Location:1290 → 1342

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

pfam00520
Location:592 → 808

Ion_trans; Ion transport protein

pfam06512
Location:813 → 1030

Na_trans_assoc; Sodium ion transport-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_000075.7 Reference GRCm39 C57BL/6J

Range

119582829..119654522 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017313362.3 → XP_017168851.1 sodium channel protein type 11 subunit alpha isoform X1

UniProtKB/TrEMBL

A0A0R5RP39

Conserved Domains (4) summary

cd13433
Location:1307 → 1359

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

pfam00520
Location:1051 → 1315

Ion_trans; Ion transport protein

pfam06512
Location:830 → 1047

Na_trans_assoc; Sodium ion transport-associated

pfam16905
Location:1623 → 1670

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