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

    Gene ID: 497770, updated on 9-Dec-2024

    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, Dec 2024]
    Expression
    Biased expression in Brain (RPKM 164.9), Muscle (RPKM 25.0) and 5 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See Scn3a in Genome Data Viewer
    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_086021.1Genomic Context describing neighboring genes Neighboring gene small nucleolar RNA SNORA48 Neighboring gene uncharacterized LOC134486368 Neighboring gene sodium voltage-gated channel alpha subunit 2 Neighboring gene small nucleolar RNA SNORA17

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    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

    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)

    NEW Try the new Transcript table

    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_013119.2NP_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:14201472
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11561428
      Ion_trans; Ion transport protein
      pfam06512
      Location:9491151
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:513661
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17441791
      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

    1. NC_086021.1 Reference GRCr8

      Range
      70554496..70666198 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

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

      UniProtKB/TrEMBL
      A6HLX3
      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
    2. XM_008761920.4XP_008760142.1  sodium channel protein type 3 subunit alpha isoform X5

      UniProtKB/TrEMBL
      A6HLX3
      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. XM_008761918.4XP_008760140.1  sodium channel protein type 3 subunit alpha isoform X3

      UniProtKB/TrEMBL
      A6HLX3
      Conserved Domains (6) summary
      cd13433
      Location:14231475
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11771431
      Ion_trans; Ion transport protein
      pfam06512
      Location:9521154
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:510651
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17471802
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
      cl16916
      Location:16621697
      ChtBD1; Hevein or type 1 chitin binding domain
    4. XM_039105646.2XP_038961574.1  sodium channel protein type 3 subunit alpha isoform X4

      UniProtKB/TrEMBL
      A6HLX3
      Conserved Domains (5) summary
      cd13433
      Location:14231475
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11591431
      Ion_trans; Ion transport protein
      pfam06512
      Location:9521154
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:513664
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:17471794
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    5. XM_008761916.4XP_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: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
    6. XM_008761915.4XP_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: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
    7. XM_039105647.2XP_038961575.1  sodium channel protein type 3 subunit alpha isoform X6

      Conserved Domains (5) summary
      cd13433
      Location:834886
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:570842
      Ion_trans; Ion transport protein
      pfam06512
      Location:363565
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:3875
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel
      pfam16905
      Location:11581205
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    8. XM_039105648.2XP_038961576.1  sodium channel protein type 3 subunit alpha isoform X7

      Conserved Domains (3) summary
      pfam00520
      Location:742955
      Ion_trans; Ion transport protein
      pfam06512
      Location:9811100
      Na_trans_assoc; Sodium ion transport-associated
      pfam11933
      Location:513693
      Na_trans_cytopl; Cytoplasmic domain of voltage-gated Na+ ion channel