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SCN3A sodium voltage-gated channel alpha subunit 3 [ Homo sapiens (human) ]

Gene ID: 6328, updated on 1-Jun-2020

Summary

Official Symbol
SCN3Aprovided by HGNC
Official Full Name
sodium voltage-gated channel alpha subunit 3provided by HGNC
Primary source
HGNC:HGNC:10590
See related
Ensembl:ENSG00000153253 MIM:182391
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
NAC3; EIEE62; FFEVF4; Nav1.3
Summary
Voltage-gated sodium channels are transmembrane glycoprotein complexes composed of a large alpha subunit with 24 transmembrane domains and one or more regulatory beta subunits. They 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, and is found in a cluster of five alpha subunit genes on chromosome 2. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
Expression
Biased expression in brain (RPKM 5.7), adrenal (RPKM 1.1) and 11 other tissues See more
Orthologs

Genomic context

See SCN3A in Genome Data Viewer
Location:
2q24.3
Exon count:
31
Annotation release Status Assembly Chr Location
109.20200522 current GRCh38.p13 (GCF_000001405.39) 2 NC_000002.12 (165087526..165204295, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (165944030..166060577, complement)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene RNA, 5S ribosomal pseudogene 111 Neighboring gene solute carrier family 38 member 11 Neighboring gene sodium voltage-gated channel alpha subunit 2 Neighboring gene MAPRE1 pseudogene 3 Neighboring gene cysteine and serine rich nuclear protein 3

Genomic regions, transcripts, and products

Expression

  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

HIV-1 interactions

Protein interactions

Protein Gene Interaction Pubs
Vif vif HIV-1 Vif downregulates the expression of sodium channel, voltage-gated, type III, alpha subunit (SCN3A) in Vif-expression T cells PubMed

Go to the HIV-1, Human Interaction Database

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Homology

Clone Names

  • KIAA1356

Gene Ontology Provided by GOA

Function Evidence Code Pubs
cation channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated ion channel activity IEA
Inferred from Electronic Annotation
more info
 
voltage-gated sodium channel activity IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated sodium channel activity NAS
Non-traceable Author Statement
more info
PubMed 
Process Evidence Code Pubs
membrane depolarization during action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuronal action potential IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
regulation of ion transmembrane transport IEA
Inferred from Electronic Annotation
more info
 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion transport NAS
Non-traceable Author Statement
more info
PubMed 
Component Evidence Code Pubs
axon IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
cytoplasm IEA
Inferred from Electronic Annotation
more info
 
plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
voltage-gated sodium channel complex IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 

General protein information

Preferred Names
sodium channel protein type 3 subunit alpha
Names
brain III voltage-gated sodium channel
sodium channel protein brain III subunit alpha
sodium channel protein type III subunit alpha
sodium channel, voltage gated, type III alpha subunit
sodium channel, voltage-gated, type III, alpha polypeptide
voltage-gated sodium channel subtype III
voltage-gated sodium channel subunit alpha Nav1.3

NCBI Reference Sequences (RefSeq)

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.

Genomic

  1. NG_042289.1 RefSeqGene

    Range
    5039..121563
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001081676.2NP_001075145.1  sodium channel protein type 3 subunit alpha isoform 2

    See identical proteins and their annotated locations for NP_001075145.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2), also known as 12v1, SCN3A-s, or the adult form, uses an alternate in-frame splice site in the central coding region, compared to variant 1, resulting in a shorter protein (isoform 2).
    Source sequence(s)
    AC013463, AF035686, AF225986, AJ251507, AL079365, BM681920, DA796981
    UniProtKB/Swiss-Prot
    Q9NY46
    UniProtKB/TrEMBL
    Q9C007
    Conserved Domains (6) summary
    cd13433
    Location:14201472
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11741428
    Ion_trans; Ion transport protein
    pfam06512
    Location:9491151
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510648
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17441799
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:16591694
    ChtBD1; Hevein or type 1 chitin binding domain
  2. NM_001081677.2NP_001075146.1  sodium channel protein type 3 subunit alpha isoform 3

    See identical proteins and their annotated locations for NP_001075146.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3), also known as the neonatal form, uses an alternate in-frame splice site in the central coding region and an alternate form of an exon in the 5' coding region, compared to variant 1. The resulting isoform (3) is shorter than isoform 1, and contains one amino acid substitution relative to isoform 2.
    Source sequence(s)
    AC013463, AF035686, AJ251507, AL079365, BM681920, DA772987
    Consensus CDS
    CCDS46440.1
    UniProtKB/Swiss-Prot
    Q9NY46
    Related
    ENSP00000386726.3, ENST00000409101.7
    Conserved Domains (6) summary
    cd13433
    Location:14201472
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:11741428
    Ion_trans; Ion transport protein
    pfam06512
    Location:9491151
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510648
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17441799
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:16591694
    ChtBD1; Hevein or type 1 chitin binding domain
  3. NM_006922.4NP_008853.3  sodium channel protein type 3 subunit alpha isoform 1

    See identical proteins and their annotated locations for NP_008853.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1), also known as 12v4, represents the longest transcript and encodes the longest isoform (1).
    Source sequence(s)
    AC013463, AF035686, AF225987, AJ251507, AL079365, BM681920, DA796981
    Consensus CDS
    CCDS33312.1
    UniProtKB/Swiss-Prot
    Q9NY46
    Related
    ENSP00000283254.7, ENST00000283254.12
    Conserved Domains (6) summary
    cd13433
    Location:14691521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12231477
    Ion_trans; Ion transport protein
    pfam06512
    Location:9981200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17931848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:17081743
    ChtBD1; Hevein or type 1 chitin binding domain

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p13 Primary Assembly

    Range
    165087526..165204295 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011511613.3XP_011509915.1  sodium channel protein type 3 subunit alpha isoform X5

    Conserved Domains (5) summary
    cd13433
    Location:839891
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:593847
    Ion_trans; Ion transport protein
    pfam06512
    Location:368570
    Na_trans_assoc; Sodium ion transport-associated
    pfam16905
    Location:11631218
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:10781113
    ChtBD1; Hevein or type 1 chitin binding domain
  2. XM_017004662.2XP_016860151.1  sodium channel protein type 3 subunit alpha isoform X4

  3. XM_017004661.2XP_016860150.1  sodium channel protein type 3 subunit alpha isoform X3

    Related
    ENSP00000492251.1, ENST00000639244.1
    Conserved Domains (6) summary
    cd13433
    Location:14521504
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12061460
    Ion_trans; Ion transport protein
    pfam06512
    Location:9811183
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17761831
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:16911726
    ChtBD1; Hevein or type 1 chitin binding domain
  4. XM_017004660.2XP_016860149.1  sodium channel protein type 3 subunit alpha isoform X2

    UniProtKB/Swiss-Prot
    Q9NY46
    Related
    ENSP00000353206.3, ENST00000360093.7
    Conserved Domains (6) summary
    cd13433
    Location:14691521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12231477
    Ion_trans; Ion transport protein
    pfam06512
    Location:9981200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17931848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:17081743
    ChtBD1; Hevein or type 1 chitin binding domain
  5. XM_017004663.2XP_016860152.1  sodium channel protein type 3 subunit alpha isoform X5

    Conserved Domains (5) summary
    cd13433
    Location:839891
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:593847
    Ion_trans; Ion transport protein
    pfam06512
    Location:368570
    Na_trans_assoc; Sodium ion transport-associated
    pfam16905
    Location:11631218
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:10781113
    ChtBD1; Hevein or type 1 chitin binding domain
  6. XM_011511610.3XP_011509912.1  sodium channel protein type 3 subunit alpha isoform X1

    See identical proteins and their annotated locations for XP_011509912.1

    UniProtKB/Swiss-Prot
    Q9NY46
    Conserved Domains (6) summary
    cd13433
    Location:14691521
    Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
    pfam00520
    Location:12231477
    Ion_trans; Ion transport protein
    pfam06512
    Location:9981200
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
    pfam16905
    Location:17931848
    GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    cl16916
    Location:17081743
    ChtBD1; Hevein or type 1 chitin binding domain
  7. XM_017004666.1XP_016860155.1  sodium channel protein type 3 subunit alpha isoform X8

  8. XM_017004665.1XP_016860154.1  sodium channel protein type 3 subunit alpha isoform X7

    Related
    ENSP00000499420.1, ENST00000668657.1
  9. XM_017004664.1XP_016860153.1  sodium channel protein type 3 subunit alpha isoform X6

    Related
    ENSP00000492807.1, ENST00000640652.1
    Conserved Domains (3) summary
    pfam00520
    Location:143434
    Ion_trans; Ion transport protein
    pfam06512
    Location:9981117
    Na_trans_assoc; Sodium ion transport-associated
    pfam11933
    Location:510629
    Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
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