U.S. flag

An official website of the United States government

Format

Send to:

Choose Destination

Links from Nucleotide

    • Showing Current items.

    SCN11A sodium voltage-gated channel alpha subunit 11 [ Homo sapiens (human) ]

    Gene ID: 11280, updated on 28-Oct-2024

    Summary

    Official Symbol
    SCN11Aprovided by HGNC
    Official Full Name
    sodium voltage-gated channel alpha subunit 11provided by HGNC
    Primary source
    HGNC:HGNC:10583
    See related
    Ensembl:ENSG00000168356 MIM:604385; AllianceGenome:HGNC:10583
    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
    NaN; PN5; FEPS3; HSAN7; SNS-2; NAV1.9; SCN12A
    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 highly expressed in nociceptive neurons of dorsal root ganglia and trigeminal ganglia. It mediates brain-derived neurotrophic factor-evoked membrane depolarization and is a major effector of peripheral inflammatory pain hypersensitivity. Mutations in this gene have been associated with hereditary sensory and autonomic neuropathy type VII and familial episodic pain syndrome-3. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Mar 2017]
    Expression
    Biased expression in spleen (RPKM 1.9), placenta (RPKM 0.6) and 13 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See SCN11A in Genome Data Viewer
    Location:
    3p22.2
    Exon count:
    35
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (38845764..39051944, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (38857981..39064106, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38887255..39093435, complement)

    Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene sodium voltage-gated channel alpha subunit 10 Neighboring gene uncharacterized LOC105377034 Neighboring gene uncharacterized LOC107986042 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14215 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr3:38877996-38878572 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr3:38912374-38913573 Neighboring gene NANOG hESC enhancer GRCh37_chr3:39020389-39020890 Neighboring gene RNA, U6 small nuclear 1227, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:39092668-39093540 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14216 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19690 Neighboring gene WD repeat domain 48 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:39144473-39144972 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14217 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14218 Neighboring gene ReSE screen-validated silencer GRCh37_chr3:39166834-39167009 Neighboring gene golgi reassembly stacking protein 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr3:39177733-39178638 Neighboring gene tetratricopeptide repeat domain 21A Neighboring gene microRNA 6822

    Genomic regions, transcripts, and products

    Expression

    • Project title: HPA RNA-seq normal tissues 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?

    Phenotypes

    EBI GWAS Catalog

    Description
    Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
    EBI GWAS Catalog

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables voltage-gated sodium channel activity IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables voltage-gated sodium channel activity IDA
    Inferred from Direct Assay
    more info
    PubMed 
    enables voltage-gated sodium channel activity IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    Process Evidence Code Pubs
    involved_in action potential initiation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in acute inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in artery development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in axonogenesis IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in behavioral response to acetic acid induced pain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in behavioral response to formalin induced pain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cAMP/PKA signal transduction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in calcitonin gene-related peptide receptor signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in calcium ion transmembrane transport IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cardiac muscle cell action potential involved in contraction IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in cell motility IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cellular response to cold IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in chronic inflammatory response IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in circadian rhythm IEA
    Inferred from Electronic Annotation
    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 temperature stimulus involved in sensory perception of pain IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in mast cell degranulation IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in membrane depolarization during action potential IDA
    Inferred from Direct Assay
    more info
    PubMed 
    involved_in membrane depolarization during action potential IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in micturition IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in neuronal action potential IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in reflex IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to auditory stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to heat IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to high light intensity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to nitric oxide IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to prostaglandin E IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to toxic substance IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in response to xenobiotic stimulus IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of itch IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sensory perception of pain IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    involved_in sensory perception of pain ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    involved_in skeletal muscle organ development IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in small intestine smooth muscle contraction IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in sodium ion transmembrane transport IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in thermosensory behavior IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in thigmotaxis IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in C-fiber IEA
    Inferred from Electronic Annotation
    more info
     
    located_in axon ISS
    Inferred from Sequence or Structural Similarity
    more info
     
    located_in axonal growth cone IEA
    Inferred from Electronic Annotation
    more info
     
    located_in extracellular exosome HDA PubMed 
    located_in neuronal cell body IEA
    Inferred from Electronic Annotation
    more info
     
    is_active_in plasma membrane IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in plasma membrane IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    part_of voltage-gated sodium channel complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    sodium channel protein type 11 subunit alpha
    Names
    peripheral nerve sodium channel 5
    sensory neuron sodium channel 2
    sodium channel protein type XI subunit alpha
    sodium channel, voltage-gated, type XI, alpha polypeptide
    sodium channel, voltage-gated, type XI, alpha subunit
    sodium channel, voltage-gated, type XII, alpha polypeptide
    voltage-gated sodium channel subunit alpha Nav1.9

    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.

    Genomic

    1. NG_033859.2 RefSeqGene

      Range
      5043..211223
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001349253.2NP_001336182.1  sodium channel protein type 11 subunit alpha

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) represents the longer transcript. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC116038, AC123903
      Consensus CDS
      CCDS33737.1
      UniProtKB/Swiss-Prot
      A6NN05, C9JD48, C9JR31, Q68K15, Q8NDX3, Q9UHE0, Q9UHM0, Q9UI33
      UniProtKB/TrEMBL
      A0A6Q8PGN4
      Related
      ENSP00000307599.3, ENST00000302328.9
      Conserved Domains (4) summary
      cd13433
      Location:13091361
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10551317
      Ion_trans; Ion transport protein
      pfam06512
      Location:8281051
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:16181678
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    2. NM_014139.3NP_054858.2  sodium channel protein type 11 subunit alpha

      See identical proteins and their annotated locations for NP_054858.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR compared to variant 1. Both variants 1 and 2 encode the same protein.
      Source sequence(s)
      AC116038, AC123903
      Consensus CDS
      CCDS33737.1
      UniProtKB/Swiss-Prot
      A6NN05, C9JD48, C9JR31, Q68K15, Q8NDX3, Q9UHE0, Q9UHM0, Q9UI33
      UniProtKB/TrEMBL
      A0A6Q8PGN4
      Related
      ENSP00000416757.3, ENST00000456224.7
      Conserved Domains (4) summary
      cd13433
      Location:13091361
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10551317
      Ion_trans; Ion transport protein
      pfam06512
      Location:8281051
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:16181678
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated

    RNA

    1. NR_164473.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AC123903

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

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

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000003.12 Reference GRCh38.p14 Primary Assembly

      Range
      38845764..39051944 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047447378.1XP_047303334.1  sodium channel protein type 11 subunit alpha isoform X1

    2. XM_017005650.2XP_016861139.1  sodium channel protein type 11 subunit alpha isoform X2

      UniProtKB/Swiss-Prot
      A6NN05, C9JD48, C9JR31, Q68K15, Q8NDX3, Q9UHE0, Q9UHM0, Q9UI33
      UniProtKB/TrEMBL
      A0A6Q8PGN4
      Conserved Domains (4) summary
      cd13433
      Location:13091361
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:10551317
      Ion_trans; Ion transport protein
      pfam06512
      Location:8281051
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:16181678
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
    3. XM_017005651.2XP_016861140.1  sodium channel protein type 11 subunit alpha isoform X3

      UniProtKB/TrEMBL
      A0A6Q8PGN4
    4. XM_011533321.3XP_011531623.1  sodium channel protein type 11 subunit alpha isoform X4

      UniProtKB/TrEMBL
      A0A6Q8PGN4
      Conserved Domains (5) summary
      cd13433
      Location:10881140
      Na_channel_gate; Inactivation gate of the voltage-gated sodium channel alpha subunits
      pfam00520
      Location:11621394
      Ion_trans; Ion transport protein
      pfam06512
      Location:607830
      Na_trans_assoc; Sodium ion transport-associated
      pfam16905
      Location:14031457
      GPHH; Voltage-dependent L-type calcium channel, IQ-associated
      cl21478
      Location:159214
      ATP-synt_B; ATP synthase B/B' CF(0)
    5. XM_017005653.2XP_016861142.1  sodium channel protein type 11 subunit alpha isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060927.1 Alternate T2T-CHM13v2.0

      Range
      38857981..39064106 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054345105.1XP_054201080.1  sodium channel protein type 11 subunit alpha isoform X1

    2. XM_054345106.1XP_054201081.1  sodium channel protein type 11 subunit alpha isoform X2

      UniProtKB/Swiss-Prot
      A6NN05, C9JD48, C9JR31, Q68K15, Q8NDX3, Q9UHE0, Q9UHM0, Q9UI33
    3. XM_054345107.1XP_054201082.1  sodium channel protein type 11 subunit alpha isoform X3

    4. XM_054345108.1XP_054201083.1  sodium channel protein type 11 subunit alpha isoform X4

    5. XM_054345109.1XP_054201084.1  sodium channel protein type 11 subunit alpha isoform X5

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_001287223.1: Suppressed sequence

      Description
      NM_001287223.1: This RefSeq was removed because it is partial at the 5' end.