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

    Gene ID: 20265, updated on 2-Nov-2024

    Summary

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    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 membrane depolarization during action potential. Acts upstream of or within several processes, including adult walking behavior; determination of adult lifespan; and neuronal action potential. Located in several cellular components, including T-tubule; Z disc; and main axon. Part of sodium channel complex. Is expressed in several structures, including heart and nervous system. 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 6B; 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, Nov 2024]
    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

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    See Scn1a in Genome Data Viewer
    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_000068.8Genomic Context describing neighboring genes Neighboring gene polypeptide N-acetylgalactosaminyltransferase 3 Neighboring gene STARR-seq mESC enhancer starr_04695 Neighboring gene tetratricopeptide repeat domain 21B Neighboring gene STARR-positive B cell enhancer mm9_chr2:66094546-66094847 Neighboring gene predicted gene 13630 Neighboring gene ribosomal protein L35, pseudogene 1 Neighboring gene predicted gene 13629 Neighboring gene sodium channel, voltage-gated, type IX, alpha Neighboring gene predicted gene, 35265

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Mouse ENCODE transcriptome data 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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    Related articles in PubMed

    1. C57BL/6J and C57BL/6N substrains differentially influence phenotype severity in the Scn1a (+/-) mouse model of Dravet syndrome. Kang SK, et al. Epilepsia Open, 2019 Mar. PMID 30868126, Free PMC Article
    2. Neuropathological Characterization of a Dravet Syndrome Knock-In Mouse Model Useful for Investigating Cannabinoid Treatments. Satta V, et al. Front Mol Neurosci, 2020. PMID 33584198, Free PMC Article
    3. Altered expression of voltage gated sodium channel Nav1.1 is involved in motor ability in MPTP-treated mice. Liu W, et al. Brain Res Bull, 2021 May. PMID 33610724
    4. Na(V)1.1 channels are critical for intercellular communication in the suprachiasmatic nucleus and for normal circadian rhythms. Han S, et al. Proc Natl Acad Sci U S A, 2012 Feb 7. PMID 22223655, Free PMC Article
    5. Potentiating α(2) subunit containing perisomatic GABA(A) receptors protects against seizures in a mouse model of Dravet syndrome. Nomura T, et al. J Physiol, 2019 Aug. PMID 31045243, Free PMC Article

    See all (201) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. 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.
    2. 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.
    3. 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.
    4. 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.
    5. 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.
    6. 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.
    7. Behavioral phenotyping of young Scn1a haploinsufficient mice.
      Title: Behavioral phenotyping of young Scn1a haploinsufficient mice.
    8. 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.
    9. 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.
    10. 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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by MGI

    Function Evidence Code Pubs
    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 IEA
    Inferred from Electronic Annotation
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 regulation of presynaptic membrane potential IEA
    Inferred from Electronic Annotation
    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
    		  
    acts_upstream_of_or_within sodium ion transport IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    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 
    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 IEA
    Inferred from Electronic Annotation
    more info
    		  
    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 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 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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    NEW Try the new Transcript table

    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)

    1. 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

    2. 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

    1. NC_000068.8 Reference GRCm39 C57BL/6J

      Range
      66101125..66271181 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. 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

    2. 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

    3. 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

    RNA

    1. XR_001781558.3 RNA Sequence

    2. XR_001781559.3 RNA Sequence

    Nucleotide Protein Strain
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    A2APX8.1 GenPept UniProtKB/Swiss-Prot:A2APX8

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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