Scn3a sodium voltage-gated channel alpha subunit 3 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Scn3aprovided by RGD
Official Full Name: sodium voltage-gated channel alpha subunit 3provided by RGD
Primary source: RGD:3635
See related: EnsemblRapid:ENSRNOG00000005007 AllianceGenome:RGD:3635
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: SCIII; Scn2a; Nav1.3
Summary: Enables calmodulin binding activity. Involved in cellular response to antibiotic; nervous system development; and response to pyrethroid. Located in axon and neuronal cell body. Human ortholog(s) of this gene implicated in developmental and epileptic encephalopathy 62 and familial focal epilepsy with variable foci 4. Orthologous to human SCN3A (sodium voltage-gated channel alpha subunit 3). [provided by Alliance of Genome Resources, Nov 2024]
Expression: Biased expression in Brain (RPKM 164.9), Muscle (RPKM 25.0) and 5 other tissues 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 (70554496..70666198, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	3	NC_051338.1 (50146411..50258119, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	3	NC_005102.4 (51530897..51643140, 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?

Exploring the mechanism of Nav1.3 in the ION-CCI rat model based on the TLR4/TRAF6/NF-kappaB pathway.
Title: Exploring the mechanism of Nav1.3 in the ION-CCI rat model based on the TLR4/TRAF6/NF-κB pathway.
Knockdown of rno_circRNA_009194 Improves Outcomes in Traumatic Brain Injury Rats through Inhibiting Voltage-Gated Sodium Channel Nav1.3.
Title: Knockdown of rno_circRNA_009194 Improves Outcomes in Traumatic Brain Injury Rats through Inhibiting Voltage-Gated Sodium Channel Nav1.3.
MiR-214-3p plays a protective role in diabetic neuropathic rats by regulating Nav1.3 and TLR4.
Title: MiR-214-3p plays a protective role in diabetic neuropathic rats by regulating Nav1.3 and TLR4.
Nav1.3 and FGF14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells.
Title: Nav1.3 and FGF14 are primary determinants of the TTX-sensitive sodium current in mouse adrenal chromaffin cells.
Chronic constriction injury gives rise to an up-regulation of Nav1.3 in trigeminal nerve and C-type neurons at the trigeminal ganglion.
Title: The expression of voltage-gated sodium channels in trigeminal nerve following chronic constriction injury in rats.
showed that Nav1.3 at mRNA and protein levels was abundantly re-expressed in the ipsilateral and contralateral SN at 49 days postlesion
Title: Re-expression of voltage-gated sodium channel subtype Nav1.3 in the substantia nigra after dopamine depletion.
the protein expressions of voltage-gated sodium channels (VGSCs) alpha-subunits Nav1.3, Nav1.7 and Nav1.9 increased in dorsal root ganglionof diabetic rats and were normalized by TIIA application.
Title: Tanshinone IIA Improves Painful Diabetic Neuropathy by Suppressing the Expression and Activity of Voltage-Gated Sodium Channel in Rat Dorsal Root Ganglia.
EA attenuates SCI-induced Nav1.3 and Bax upregulation in injured spinal cord via upregulating miR-214.
Title: Electro-acupuncture-modulated miR-214 prevents neuronal apoptosis by targeting Bax and inhibits sodium channel Nav1.3 expression in rats after spinal cord injury.
Study found that trigeminal ganglion in rats subjected to an infraorbital nerve-chronic constriction injury showed upregulation of Nav1.3 and downregulation of Nav1.7, Nav1.8, and Nav1.9 messenger RNA and protein levels. Findings suggest that voltage-gated sodium channels may participate in the regulation of trigeminal neuralgia.
Title: Changes in the expression of voltage-gated sodium channels Nav1.3, Nav1.7, Nav1.8, and Nav1.9 in rat trigeminal ganglia following chronic constriction injury.
We used a validated recombinant adeno-associated virus (AAV)-shRNA-Nav1.3 vector to knockdown expression of Nav1.3, via a clinically applicable intrathecal injection method.
Title: Virus-Mediated Knockdown of Nav1.3 in Dorsal Root Ganglia of STZ-Induced Diabetic Rats Alleviates Tactile Allodynia.

Submit: New GeneRIF Correction See all GeneRIFs (21)

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

RH139649 (e-PCR)
- UniSTS:221733

RH94597 (e-PCR)
- UniSTS:119845

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

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

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables calmodulin binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables voltage-gated sodium channel activity	IBA Inferred from Biological aspect of Ancestor more info
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
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 behavioral response to pain	IEA Inferred from Electronic Annotation more info
involved_in behavioral response to pain	ISO Inferred from Sequence Orthology more info
involved_in cellular response to antibiotic	IDA Inferred from Direct Assay 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	IEA Inferred from Electronic Annotation more info
involved_in membrane depolarization during action potential	ISO Inferred from Sequence Orthology more info
involved_in nervous system development	IEP Inferred from Expression Pattern more info	PubMed
involved_in neuronal action potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in response to pyrethroid	IDA Inferred from Direct Assay more info	PubMed
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

Component	Evidence Code	Pubs
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 basal plasma membrane	IEA Inferred from Electronic Annotation more info
located_in membrane	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	IDA Inferred from Direct Assay more info	PubMed
is_active_in plasma membrane	ISO Inferred from Sequence Orthology more info
located_in sarcoplasm	IEA Inferred from Electronic Annotation more info
located_in sarcoplasm	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
part_of voltage-gated sodium channel complex	ISO Inferred from Sequence Orthology more info
part_of voltage-gated sodium channel complex	TAS Traceable Author Statement more info	PubMed

General protein information

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Preferred Names: sodium channel protein type 3 subunit alpha

Names: rCG26412-like; sodium channel protein type 3 subunit alpha-like; sodium channel protein type III subunit alpha; sodium channel protein, brain III subunit alpha; sodium channel, voltage-gated, type 3, alpha subunit; sodium channel, voltage-gated, type III, alpha subunit; voltage-gated sodium channel subtype III; voltage-gated sodium channel subunit alpha Nav1.3

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_013119.2 → NP_037251.2 sodium channel protein type 3 subunit alpha

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000003

UniProtKB/TrEMBL

A6HLX3

Related

ENSRNOP00000006646.8, ENSRNOT00000006646.9

Conserved Domains (5) summary

cd13433
Location:1420 → 1472

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

pfam00520
Location:1156 → 1428

Ion_trans; Ion transport protein

pfam06512
Location:949 → 1151

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:513 → 661

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

pfam16905
Location:1744 → 1791

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

70554496..70666198 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017591972.3 → XP_017447461.1 sodium channel protein type 3 subunit alpha isoform X1

UniProtKB/TrEMBL

A6HLX3

Conserved Domains (6) summary

cd13433
Location:1452 → 1504

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

pfam00520
Location:1206 → 1460

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1183

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 629

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

pfam16905
Location:1776 → 1831

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

cl16916
Location:1691 → 1726

ChtBD1; Hevein or type 1 chitin binding domain
XM_008761920.4 → XP_008760142.1 sodium channel protein type 3 subunit alpha isoform X5

UniProtKB/TrEMBL

A6HLX3

Conserved Domains (6) summary

cd13433
Location:1420 → 1472

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

pfam00520
Location:1174 → 1428

Ion_trans; Ion transport protein

pfam06512
Location:949 → 1151

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 648

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

pfam16905
Location:1744 → 1799

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

cl16916
Location:1659 → 1694

ChtBD1; Hevein or type 1 chitin binding domain
XM_008761918.4 → XP_008760140.1 sodium channel protein type 3 subunit alpha isoform X3

UniProtKB/TrEMBL

A6HLX3

Conserved Domains (6) summary

cd13433
Location:1423 → 1475

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

pfam00520
Location:1177 → 1431

Ion_trans; Ion transport protein

pfam06512
Location:952 → 1154

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 651

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

pfam16905
Location:1747 → 1802

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

cl16916
Location:1662 → 1697

ChtBD1; Hevein or type 1 chitin binding domain
XM_039105646.2 → XP_038961574.1 sodium channel protein type 3 subunit alpha isoform X4

UniProtKB/TrEMBL

A6HLX3

Conserved Domains (5) summary

cd13433
Location:1423 → 1475

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

pfam00520
Location:1159 → 1431

Ion_trans; Ion transport protein

pfam06512
Location:952 → 1154

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:513 → 664

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

pfam16905
Location:1747 → 1794

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_008761916.4 → XP_008760138.1 sodium channel protein type 3 subunit alpha isoform X2

UniProtKB/TrEMBL

A0A0G2K237, A6HLX3

Related

ENSRNOP00000072091.2, ENSRNOT00000081401.3

Conserved Domains (6) summary

cd13433
Location:1452 → 1504

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

pfam00520
Location:1206 → 1460

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1183

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 629

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

pfam16905
Location:1776 → 1831

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

cl16916
Location:1691 → 1726

ChtBD1; Hevein or type 1 chitin binding domain
XM_008761915.4 → XP_008760137.1 sodium channel protein type 3 subunit alpha isoform X1

See identical proteins and their annotated locations for XP_008760137.1

UniProtKB/TrEMBL

A6HLX3

Conserved Domains (6) summary

cd13433
Location:1452 → 1504

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

pfam00520
Location:1206 → 1460

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1183

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:510 → 629

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

pfam16905
Location:1776 → 1831

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

cl16916
Location:1691 → 1726

ChtBD1; Hevein or type 1 chitin binding domain
XM_039105647.2 → XP_038961575.1 sodium channel protein type 3 subunit alpha isoform X6

Conserved Domains (5) summary

cd13433
Location:834 → 886

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

pfam00520
Location:570 → 842

Ion_trans; Ion transport protein

pfam06512
Location:363 → 565

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:38 → 75

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

pfam16905
Location:1158 → 1205

GPHH; Voltage-dependent L-type calcium channel, IQ-associated
XM_039105648.2 → XP_038961576.1 sodium channel protein type 3 subunit alpha isoform X7

Conserved Domains (3) summary

pfam00520
Location:742 → 955

Ion_trans; Ion transport protein

pfam06512
Location:981 → 1100

Na_trans_assoc; Sodium ion transport-associated

pfam11933
Location:513 → 693

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