Scn2a sodium voltage-gated channel alpha subunit 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scn2aprovided by RGD
Official Full Name: sodium voltage-gated channel alpha subunit 2provided by RGD
Primary source: RGD:3632
See related: Ensembl:ENSRNOG00000005018 AllianceGenome:RGD:3632
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
Also known as: SCN; ScpII; NachII; Nav1.2; Scn2a1; Scn2a2; RII/RIIA; RNSCPIIR
Summary: Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with four repeat domains, each of which is composed of six membrane-spanning segments, and one or more regulatory beta subunits. Voltage-gated sodium channels are responsible for the generation and propagation of action potentials in neurons and muscle. This gene encodes one member of the sodium channel alpha subunit gene family. In humans, variants of this gene are associated with seizure disorders and autism spectrum disorder. Mice homozygous for a knockout mutation die with severe hypoxia and extensive neuronal cell death, while gain of function mutations result in progressive seizure disorder. [provided by RefSeq, Nov 2016]
Expression: Restricted expression toward (RPKM 552.3) See more
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Genomic context

Location:: 3q21

Exon count:: 29

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	3	NC_086021.1 (70710862..70845569)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (50302781..50437504)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (51687910..51822008)

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?

Scorpion toxin MeuNaTxalpha-1 sensitizes primary nociceptors by selective modulation of voltage-gated sodium channels.
Title: Scorpion toxin MeuNaTxα-1 sensitizes primary nociceptors by selective modulation of voltage-gated sodium channels.
The Nav1.2 are highly expressed in axon terminals in central hilus compared to stratum radiatum and in dendrites and spines in stratum radiatum compared to central hilus .
Title: Sodium channel subtypes are differentially localized to pre- and post-synaptic sites in rat hippocampus.
Knockdown of Nav1.2 channels in pre-oligodendrocyte alters their morphology, reduces axon-oligodendrocyte interactions and impairs myelination.
Title: Oligodendroglial excitability mediated by glutamatergic inputs and Nav1.2 activation.
Here, the authors show that hypoxia activates the Small Ubiquitin-like Modifier (SUMO) pathway in rat cerebellar granule neurons (CGN) and that SUMOylation of NaV1.2 channels increases sodium current.
Title: SUMOylation of Na(V)1.2 channels mediates the early response to acute hypoxia in central neurons.
The polarity of (Ca(2+))2-CaMC relative to the IQ motif of NaV1.2 was opposite to that seen in apo CaMC-Nav1.2IQp (2KXW), revealing that CaMC recognizes nested, anti-parallel sites in Nav1.2IQp. (CaMC is C-domain residues of CaM, calmodulin).
Title: Calcium triggers reversal of calmodulin on nested anti-parallel sites in the IQ motif of the neuronal voltage-dependent sodium channel Na(V)1.2.
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.
Fibroblast growth factor 12 is a component of the voltage-gated sodium channel 1.2 (nav1.2) macromolecular complex in the rat brain.
Title: Quantitative proteomics reveals protein-protein interactions with fibroblast growth factor 12 as a component of the voltage-gated sodium channel 1.2 (nav1.2) macromolecular complex in Mammalian brain.
In NaV1.2, Cys910 is disulfide-bonded to Cys918 and Cys912.
Title: Probing the Redox States of Sodium Channel Cysteines at the Binding Site of μO§-Conotoxin GVIIJ.
Reciprocal regulation of phosphorylation and MeArg of Nav1.2 may underlie changes in neuronal Nav channel function in response to seizures and also contribute to physiological modulation of neuronal excitability.
Title: Reciprocal changes in phosphorylation and methylation of mammalian brain sodium channels in response to 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 (25)

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

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

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

D3Mit8 (e-PCR), detects polymorphism
- UniSTS:119587

D3Rat240 (e-PCR), detects polymorphism
- UniSTS:227625

RH94610 (e-PCR)
- UniSTS:119858

RH138915 (e-PCR)
- UniSTS:221002

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

D3Wox10 (e-PCR)
- UniSTS:240525

D3Wox14 (e-PCR)
- UniSTS:517786

d3arb7 (e-PCR)
- UniSTS:121773

D3Wox9 (e-PCR)
- UniSTS:142318

D2Kyo1 (e-PCR), detects polymorphism
- UniSTS:142318

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calmodulin binding	IEA Inferred from Electronic Annotation more info
enables calmodulin binding	ISO Inferred from Sequence Orthology more info
enables leucine zipper domain binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables sodium ion binding	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	IMP Inferred from Mutant Phenotype more info	PubMed
enables voltage-gated monoatomic ion channel activity involved in regulation of presynaptic membrane potential	NAS Non-traceable Author Statement more info	PubMed
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	IDA Inferred from Direct Assay more info	PubMed
enables voltage-gated sodium channel activity	IEA Inferred from Electronic Annotation more info
enables voltage-gated sodium channel activity	ISO Inferred from Sequence Orthology more info

Process	Evidence Code	Pubs
involved_in axon development	IEP Inferred from Expression Pattern more info	PubMed
involved_in cellular response to hypoxia	IDA Inferred from Direct Assay more info	PubMed
involved_in cerebral cortex development	IEP Inferred from Expression Pattern more info	PubMed
involved_in corpus callosum development	IEP Inferred from Expression Pattern more info	PubMed
involved_in dentate gyrus development	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within dentate gyrus development	ISO Inferred from Sequence Orthology 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 intrinsic apoptotic signaling pathway in response to osmotic stress	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to osmotic stress	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within intrinsic apoptotic signaling pathway in response to osmotic stress	ISS Inferred from Sequence or Structural Similarity more info
involved_in membrane depolarization during action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in memory	IEA Inferred from Electronic Annotation more info
involved_in memory	ISO Inferred from Sequence Orthology more info
involved_in memory	ISS Inferred from Sequence or Structural Similarity more info
involved_in myelination	IEP Inferred from Expression Pattern more info	PubMed
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
acts_upstream_of_or_within nervous system development	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within nervous system development	ISS Inferred from Sequence or Structural Similarity more info
involved_in neuron apoptotic process	IEA Inferred from Electronic Annotation more info
acts_upstream_of_or_within neuron apoptotic process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuron apoptotic process	ISS Inferred from Sequence or Structural Similarity 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	ISO Inferred from Sequence Orthology more info
involved_in neuronal action potential	TAS Traceable Author Statement more info	PubMed
involved_in optic nerve development	IEP Inferred from Expression Pattern 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	IDA Inferred from Direct Assay more info	PubMed
involved_in sodium ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in sodium ion transmembrane transport	ISO Inferred from Sequence Orthology more info
involved_in sodium ion transport	IDA Inferred from Direct Assay more info	PubMed
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
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	ISO Inferred from Sequence Orthology more info
located_in axon initial segment	IDA Inferred from Direct Assay more info	PubMed
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in glutamatergic synapse	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 node of Ranvier	IDA Inferred from Direct Assay more info	PubMed
located_in paranode region of axon	IEA Inferred from Electronic Annotation more info
located_in paranode region of axon	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation 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	IDA Inferred from Direct Assay more info	PubMed
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 2 subunit alpha

Names: RIIA sodium channel protein; sodium channel protein type II subunit alpha; sodium channel protein, brain II subunit alpha; sodium channel voltage-gated type II alpha polypeptide; sodium channel, voltage-gated, type 2, alpha 1 polypeptide; sodium channel, voltage-gated, type 2, alpha 1 subunit; sodium channel, voltage-gated, type II, alpha 1; sodium channel, voltage-gated, type II, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.2

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_012647.3 → NP_036779.2 sodium channel protein type 2 subunit alpha

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A0A8I5YBA6, A6HLX5

Related

ENSRNOP00000076431.1, ENSRNOT00000098856.1

Conserved Domains (5) summary

cd13433
Location:1474 → 1526

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

pfam00520
Location:1207 → 1482

Ion_trans; Ion transport protein

pfam06512
Location:997 → 1203

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:516 → 709

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

pfam16905
Location:1798 → 1845

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

70710862..70845569

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_063283106.1 → XP_063139176.1 sodium channel protein type 2 subunit alpha isoform X2

UniProtKB/TrEMBL

A0A0G2K207
XM_063283105.1 → XP_063139175.1 sodium channel protein type 2 subunit alpha isoform X1

UniProtKB/TrEMBL

A0A8I5YBA6
XM_063283107.1 → XP_063139177.1 sodium channel protein type 2 subunit alpha isoform X2

UniProtKB/TrEMBL

A0A0G2K207