Scn1a sodium voltage-gated channel alpha subunit 1 [Rattus norvegicus (Norway rat)] - Gene

Summary

Symbol: Scn1aprovided by RGD
Full Name: sodium voltage-gated channel alpha subunit 1provided by RGD
Primary source: RGD:69364
See related: EnsemblRapid:ENSRNOG00000053122 AllianceGenome:RGD:69364
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Summary: Enables voltage-gated sodium channel activity. Involved in neuronal action potential. Is active in presynaptic membrane. 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, Dec 2024]
Expression: Biased expression in Brain (RPKM 308.6), Heart (RPKM 37.9) and 1 other tissue See more
Orthologs: human mouse all
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Genomic context

Location:: 3q21

Exon count:: 30

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (71360840..71479870, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (50952790..51071804, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (52388811..52533365, complement)

Chromosome 3 - NC_086021.1 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: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Focal Dorsal Hippocampal Nav1.1 Knock Down Alters Place Cell Temporal Coordination and Spatial Behavior.
Title: Focal Dorsal Hippocampal Nav1.1 Knock Down Alters Place Cell Temporal Coordination and Spatial Behavior.
Scn1a and Cacna1a mutations mutually alter their original phenotypes in rats.
Title: Scn1a and Cacna1a mutations mutually alter their original phenotypes in rats.
Response of Voltage-Gated Sodium and Calcium Channels Subtypes on Dehydroepiandrosterone Treatment in Iron-Induced Epilepsy.
Title: Response of Voltage-Gated Sodium and Calcium Channels Subtypes on Dehydroepiandrosterone Treatment in Iron-Induced Epilepsy.
the presences of Nav1.1, Nav1.6, Navbeta1 and Navbeta3 mRNA and their reduced levels in rat SAN during aging.
Title: Age-dependent alterations of voltage-gated Na(+) channel isoforms in rat sinoatrial node.
Nav1.1 in facilitates fast-firing properties in medial septum neurons. Nav1.1 deficits may disrupt information processing in Dravet syndrome via a dysregulation of theta wave brain rhythms.
Title: Cognitive Deficits Associated with Nav1.1 Alterations: Involvement of Neuronal Firing Dynamics and Oscillations.
miR-9 suppressed the trafficking of Nav1.1/Nav1.2 from cytoplasm to cell membrane. miR-9 overexpression inhibited Navbeta2 expression by targeting its coding sequence domain.
Title: MicroRNA-9 induces defective trafficking of Nav1.1 and Nav1.2 by targeting Navβ2 protein coding region in rat with chronic brain hypoperfusion.
Scn1a mutant rats demonstrate a higher hyperthermia-induced seizure susceptibility than wild type rats.
Title: Inhalation of 10% carbon dioxide rapidly terminates Scn1a mutation-related hyperthermia-induced seizures.
Hyperthermia-induced seizures occurred in Scn1a mutant rats at high-frequency electroencephalographic oscillations.
Title: High-frequency EEG oscillations in hyperthermia-induced seizures of Scn1a mutant rats.
We show that reduction of Nav1.1 expression in the medial septum and diagonal band of Broca leads to a dysregulation of hippocampal oscillations in association with a spatial memory deficit
Title: Focal Scn1a knockdown induces cognitive impairment without seizures.
In the dorsal horn of the developing rat, Na(v) isoforms are developmentally regulated at the mRNA level in a subtype-specific manner, as Na(v)1.2 and Na(v)1.3 decreased significantly from P3 to adulthood, while Na(v)1.1 was upregulated during this period
Title: Transcriptional expression of voltage-gated Na⁺ and voltage-independent K⁺ channels in the developing rat superficial dorsal horn.

Submit: New GeneRIF Correction See all GeneRIFs (24)

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:516634

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

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

Scn2a1 (e-PCR), detects polymorphism
- UniSTS:516638

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

D3Rat181 (e-PCR), detects polymorphism
- UniSTS:227576

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
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	IC Inferred by Curator more info	PubMed
enables voltage-gated sodium channel activity	IEA Inferred from Electronic Annotation more info
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
enables voltage-gated sodium channel activity	TAS Traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in action potential	IEA Inferred from Electronic Annotation more info
involved_in adult walking behavior	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within adult walking behavior	ISO Inferred from Sequence Orthology more info
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	IEA Inferred from Electronic Annotation more info
involved_in detection of mechanical stimulus involved in sensory perception of pain	ISO Inferred from Sequence Orthology more info
involved_in detection of mechanical stimulus involved in sensory perception of pain	ISS Inferred from Sequence or Structural Similarity more info
involved_in determination of adult lifespan	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within determination of adult lifespan	ISO Inferred from Sequence Orthology more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within establishment of localization in cell	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in membrane depolarization during action potential	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
involved_in membrane depolarization during action potential	ISS Inferred from Sequence or Structural Similarity more info
involved_in nerve development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within nerve development	ISO Inferred from Sequence Orthology more info
involved_in neuromuscular process controlling posture	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuromuscular process controlling posture	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	IDA Inferred from Direct Assay more info	PubMed
involved_in neuronal action potential	IEA Inferred from Electronic Annotation more info
involved_in neuronal action potential	IMP Inferred from Mutant Phenotype more info	PubMed
acts_upstream_of_or_within neuronal action potential	ISO Inferred from Sequence Orthology more info
involved_in neuronal action potential	TAS Traceable Author Statement more info	PubMed
involved_in neuronal action potential propagation	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuronal action potential propagation	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within regulation of membrane potential	ISO Inferred from Sequence Orthology more info
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	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in T-tubule	IEA Inferred from Electronic Annotation more info
located_in T-tubule	ISO Inferred from Sequence Orthology more info
located_in Z disc	IEA Inferred from Electronic Annotation more info
located_in Z disc	ISO Inferred from Sequence Orthology more info
located_in Z disc	ISS Inferred from Sequence or Structural Similarity more info
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 initial segment	IEA Inferred from Electronic Annotation more info
located_in axon initial segment	ISO Inferred from Sequence Orthology more info
located_in intercalated disc	IEA Inferred from Electronic Annotation more info
located_in intercalated disc	ISO Inferred from Sequence Orthology more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IEA Inferred from Electronic Annotation more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in node of Ranvier	IEA Inferred from Electronic Annotation more info
located_in node of Ranvier	ISO Inferred from Sequence Orthology more info
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	IDA Inferred from Direct Assay more info	PubMed
part_of sodium channel complex	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 1 subunit alpha

Names: sodium channel protein type 1 subunit alpha-like; sodium channel protein type I subunit alpha; sodium channel protein, brain I subunit alpha; sodium channel, voltage-gated, type 1, alpha polypeptide; sodium channel, voltage-gated, type I, alpha polypeptide; sodium channel, voltage-gated, type I, alpha subunit; 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_030875.2 → NP_110502.2 sodium channel protein type 1 subunit alpha

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000003

UniProtKB/Swiss-Prot

P04774

UniProtKB/TrEMBL

A0A0G2K6Y2

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

RefSeqs of Annotated Genomes: GCF_036323735.1-RS_2024_02

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCr8

Genomic

NC_086021.1 Reference GRCr8

Range

71360840..71479870 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063284620.1 → XP_063140690.1 sodium channel protein type 1 subunit alpha isoform X3

UniProtKB/Swiss-Prot

P04774

Related

ENSRNOP00000074819.2, ENSRNOT00000083552.3
XM_063284619.1 → XP_063140689.1 sodium channel protein type 1 subunit alpha isoform X2

UniProtKB/Swiss-Prot

P04774
XM_063284621.1 → XP_063140691.1 sodium channel protein type 1 subunit alpha isoform X4

UniProtKB/Swiss-Prot

P04774

Related

ENSRNOP00000078175.2, ENSRNOT00000098569.2
XM_063284618.1 → XP_063140688.1 sodium channel protein type 1 subunit alpha isoform X1

UniProtKB/Swiss-Prot

P04774

UniProtKB/TrEMBL

A0A0G2K6Y2

Related

ENSRNOP00000073986.1, ENSRNOT00000091259.3
XM_063284622.1 → XP_063140692.1 sodium channel protein type 1 subunit alpha isoform X5
XM_063284623.1 → XP_063140693.1 sodium channel protein type 1 subunit alpha isoform X6