Scn1a sodium channel, voltage-gated, type I, alpha [Mus musculus (house mouse)] - Gene

Summary

Official Symbol: Scn1aprovided by MGI
Official Full Name: sodium channel, voltage-gated, type I, alphaprovided by MGI
Primary source: MGI:MGI:98246
See related: Ensembl:ENSMUSG00000064329 AllianceGenome:MGI:98246
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: Nav1.1; B230332M13
Summary: Enables voltage-gated sodium channel activity. Involved in detection of mechanical stimulus involved in sensory perception of pain and sodium ion transport. Acts upstream of or within several processes, including adult walking behavior; neuronal action potential; and neuronal action potential propagation. Located in several cellular components, including T-tubule; Z disc; and main axon. Part of sodium channel complex. Is expressed in brain; heart; sciatic nerve; sympathetic ganglion; and telencephalon. Used to study Dravet syndrome; autism spectrum disorder; and generalized epilepsy with febrile seizures plus. Human ortholog(s) of this gene implicated in Dravet syndrome; developmental and epileptic encephalopathy; familial hemiplegic migraine 3; generalized epilepsy with febrile seizures plus; and generalized epilepsy with febrile seizures plus 2. Orthologous to human SCN1A (sodium voltage-gated channel alpha subunit 1). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in cerebellum adult (RPKM 20.4), cortex adult (RPKM 13.0) and 4 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 (66101125..66271181, complement)
108.20200622	previous assembly	GRCm38.p6 (GCF_000001635.26)	2	NC_000068.7 (66270781..66440837, complement)

Chromosome 2 - NC_000068.8 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?

Temporal manipulation of the Scn1a gene reveals its essential role in adult brain function.
Title: Temporal manipulation of the Scn1a gene reveals its essential role in adult brain function.
Preferential expression of SCN1A in GABAergic neurons improves survival and epileptic phenotype in a mouse model of Dravet syndrome.
Title: Preferential expression of SCN1A in GABAergic neurons improves survival and epileptic phenotype in a mouse model of Dravet syndrome.
Persistent Nav1.1 and Nav1.6 currents drive spinal locomotor functions through nonlinear dynamics.
Title: Persistent Nav1.1 and Nav1.6 currents drive spinal locomotor functions through nonlinear dynamics.
Scn1a-GFP transgenic mouse revealed Nav1.1 expression in neocortical pyramidal tract projection neurons.
Title: Scn1a-GFP transgenic mouse revealed Nav1.1 expression in neocortical pyramidal tract projection neurons.
Astrocyte Ca[2+] signaling is facilitated in Scn1a[+/-] mouse model of Dravet syndrome.
Title: Astrocyte Ca(2+) signaling is facilitated in Scn1a(+/-) mouse model of Dravet syndrome.
Na<sub>V</sub>1.1 is essential for proprioceptive signaling and motor behaviors.
Title: Na(V)1.1 is essential for proprioceptive signaling and motor behaviors.
Behavioral phenotyping of young Scn1a haploinsufficient mice.
Title: Behavioral phenotyping of young Scn1a haploinsufficient mice.
Life-span characterization of epilepsy and comorbidities in Dravet syndrome mice carrying a targeted deletion of exon 1 of the Scn1a gene.
Title: Life-span characterization of epilepsy and comorbidities in Dravet syndrome mice carrying a targeted deletion of exon 1 of the Scn1a gene.
NaV1.1 haploinsufficiency impairs glutamatergic and GABAergic neuron function in the thalamus.
Title: Na(V)1.1 haploinsufficiency impairs glutamatergic and GABAergic neuron function in the thalamus.
Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome.
Title: Developmentally regulated impairment of parvalbumin interneuron synaptic transmission in an experimental model of Dravet syndrome.

Submit: New GeneRIF Correction See all GeneRIFs (56)

Variation

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Alleles

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

Spontaneous (1)
Targeted (13) 1 citation
Endonuclease-mediated (8) 1 citation

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

Scn1a (e-PCR), detects polymorphism
- UniSTS:516633

Scn1a (e-PCR), detects polymorphism
- UniSTS:516634

Scn1a (e-PCR), detects polymorphism
- UniSTS:516635

Scn1a (e-PCR), detects polymorphism
- UniSTS:516636

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

Scn1a (e-PCR), detects polymorphism
- UniSTS:463470

Scn1a (e-PCR), detects polymorphism
- UniSTS:463471

SCN1A_3451 (e-PCR)
- UniSTS:468677

Gene Ontology Provided by MGI

Function	Evidence Code	Pubs
enables monoatomic cation channel activity	IEA Inferred from Electronic Annotation more info
enables monoatomic ion channel activity	IEA Inferred from Electronic Annotation more info
enables sodium channel activity	IEA Inferred from Electronic Annotation more info
enables sodium ion binding	ISO Inferred from Sequence Orthology more info
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	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	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
acts_upstream_of_or_within adult walking behavior	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in cardiac muscle cell action potential involved in contraction	ISO Inferred from Sequence Orthology more info
involved_in detection of mechanical stimulus involved in sensory perception of pain	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within determination of adult lifespan	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within determination of adult lifespan	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within establishment of localization in cell	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	IDA Inferred from Direct Assay more info	PubMed
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within monoatomic ion transport	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transport	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nerve development	IGI Inferred from Genetic Interaction more info	PubMed
acts_upstream_of_or_within nerve development	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuromuscular process controlling posture	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within neuronal action potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in neuronal action potential	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuronal action potential propagation	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within regulation of membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sodium ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sodium ion transport	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in transmembrane transport	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in T-tubule	IDA Inferred from Direct Assay more info	PubMed
located_in Z disc	IDA Inferred from Direct Assay more info	PubMed
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 initial segment	IDA Inferred from Direct Assay more info	PubMed
located_in intercalated disc	IDA Inferred from Direct Assay more info	PubMed
located_in membrane	IDA Inferred from Direct Assay more info	PubMed
part_of monoatomic ion channel complex	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
located_in node of Ranvier	IDA Inferred from Direct Assay more info	PubMed
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
is_active_in presynaptic membrane	ISO Inferred from Sequence Orthology more info
part_of sodium channel complex	IPI Inferred from Physical Interaction more info	PubMed
part_of voltage-gated sodium channel complex	IBA Inferred from Biological aspect of Ancestor 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 1 subunit alpha

Names: sodium channel protein brain I subunit alpha; sodium channel protein type I subunit alpha; voltage-gated sodium channel subunit alpha Nav1.1

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_001313997.1 → NP_001300926.1 sodium channel protein type 1 subunit alpha isoform 1

Status: VALIDATED

Description

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

Source sequence(s)

AL844526, AL928726

Consensus CDS

CCDS84530.1

UniProtKB/Swiss-Prot

A2APX6, A2APX7, A2APX8, Q68V28

Conserved Domains (5) summary

cd13433
Location:1484 → 1536

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

pfam00520
Location:1217 → 1492

Ion_trans; Ion transport protein

pfam06512
Location:1006 → 1213

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 718

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

pfam16905
Location:1808 → 1855

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
NM_018733.2 → NP_061203.2 sodium channel protein type 1 subunit alpha isoform 2

See identical proteins and their annotated locations for NP_061203.2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate internal in-frame splice junction compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL844526, AL928726

Consensus CDS

CCDS38131.1

UniProtKB/Swiss-Prot

A2APX8

Related

ENSMUSP00000116881.4, ENSMUST00000138910.4

Conserved Domains (5) summary

cd13433
Location:1473 → 1525

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

pfam00520
Location:1206 → 1481

Ion_trans; Ion transport protein

pfam06512
Location:995 → 1202

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 707

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

pfam16905
Location:1797 → 1844

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

66101125..66271181 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006499027.4 → XP_006499090.1 sodium channel protein type 1 subunit alpha isoform X1

See identical proteins and their annotated locations for XP_006499090.1

UniProtKB/Swiss-Prot

A2APX6, A2APX7, A2APX8, Q68V28

Related

ENSMUSP00000107985.2, ENSMUST00000112366.8

Conserved Domains (5) summary

cd13433
Location:1484 → 1536

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

pfam00520
Location:1217 → 1492

Ion_trans; Ion transport protein

pfam06512
Location:1006 → 1213

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 718

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

pfam16905
Location:1808 → 1855

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_006499028.4 → XP_006499091.1 sodium channel protein type 1 subunit alpha isoform X2

See identical proteins and their annotated locations for XP_006499091.1

UniProtKB/Swiss-Prot

A2APX8

Conserved Domains (5) summary

cd13433
Location:1473 → 1525

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

pfam00520
Location:1206 → 1481

Ion_trans; Ion transport protein

pfam06512
Location:995 → 1202

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 707

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

pfam16905
Location:1797 → 1844

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_036159812.1 → XP_036015705.1 sodium channel protein type 1 subunit alpha isoform X3

Conserved Domains (5) summary

cd13433
Location:1390 → 1442

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

pfam00520
Location:1446 → 1702

Ion_trans; Ion transport protein

pfam06512
Location:1006 → 1213

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 718

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

pfam16905
Location:1714 → 1761

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