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

Gene ID: 11280, updated on 24-Nov-2020

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
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

Genomic context

See SCN11A in Genome Data Viewer
Location:
3p22.2
Exon count:
37
Annotation release Status Assembly Chr Location
109.20201120 current GRCh38.p13 (GCF_000001405.39) 3 NC_000003.12 (38845764..39051944, complement)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (38887260..38995136, 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 RNA, U6 small nuclear 1227, pseudogene Neighboring gene WD repeat domain 48 Neighboring gene golgi reassembly stacking protein 1 Neighboring gene tetratricopeptide repeat domain 21A Neighboring gene microRNA 6822

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?

Phenotypes

Associated conditions

Description Tests
Episodic pain syndrome, familial, 3
MedGen: C3809899 OMIM: 615552 GeneReviews: Not available
Compare labs
Neuropathy, hereditary sensory and autonomic, type VII Compare labs
Variability in the common genetic architecture of social-communication spectrum phenotypes during childhood and adolescence.
GeneReviews: Not available

General gene information

Markers

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
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 
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
 
regulation of sensory perception of pain ISS
Inferred from Sequence or Structural Similarity
more info
 
response to drug TAS
Traceable Author Statement
more info
 
sodium ion transmembrane transport IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
sodium ion transport TAS
Traceable Author Statement
more info
 
Component Evidence Code Pubs
C-fiber IEA
Inferred from Electronic Annotation
more info
 
axon ISS
Inferred from Sequence or Structural Similarity
more info
 
extracellular exosome HDA 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 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)

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
    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
    Q9UI33
    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: Homo sapiens Updated Annotation Release 109.20201120

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000003.12 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

  1. XM_017005647.1XP_016861136.1  sodium channel protein type 11 subunit alpha isoform X1

  2. XM_017005650.1XP_016861139.1  sodium channel protein type 11 subunit alpha isoform X3

    UniProtKB/Swiss-Prot
    Q9UI33
    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_017005648.1XP_016861137.1  sodium channel protein type 11 subunit alpha isoform X2

  4. XM_017005651.1XP_016861140.1  sodium channel protein type 11 subunit alpha isoform X4

  5. XM_011533321.2XP_011531623.1  sodium channel protein type 11 subunit alpha isoform X5

    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)
  6. XM_017005653.1XP_016861142.1  sodium channel protein type 11 subunit alpha isoform X7

  7. XM_017005652.1XP_016861141.1  sodium channel protein type 11 subunit alpha isoform X6

    Related
    ENSP00000502481.1, ENST00000675223.1

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.
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