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

Gene ID: 20265, updated on 10-Apr-2024

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
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Genomic context

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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Variation

Alleles

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

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

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

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)

  1. NM_001313997.1NP_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:14841536
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12171492
    Ion_trans; Ion transport protein
    pfam06512
    Location:10061213
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510718
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:18081855
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. NM_018733.2NP_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:14731525
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12061481
    Ion_trans; Ion transport protein
    pfam06512
    Location:9951202
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510707
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17971844
    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_006499027.4XP_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:14841536
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12171492
    Ion_trans; Ion transport protein
    pfam06512
    Location:10061213
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510718
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:18081855
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  2. XM_006499028.4XP_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:14731525
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12061481
    Ion_trans; Ion transport protein
    pfam06512
    Location:9951202
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510707
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17971844
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
  3. XM_036159812.1XP_036015705.1  sodium channel protein type 1 subunit alpha isoform X3

    Conserved Domains (5) summary
    cd13433
    Location:13901442
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:14461702
    Ion_trans; Ion transport protein
    pfam06512
    Location:10061213
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510718
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17141761
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated

RNA

  1. XR_001781558.3 RNA Sequence

  2. XR_001781559.3 RNA Sequence