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0SCN1A_HUMAN*   SwissProt (?) | Description Local Annotation Link Reference
General Information
NameSCN1A
DescriptionSodium channel protein type i alpha subunit (voltage-gated sodium channel alpha subunit nav1.1) (sodium channel protein, brain i alpha subunit).
SpeciesHomo sapiens (NCBI taxonomy ID: 9606)
GO0016021 integral to membrane (NAS)
0005248 voltage-gated sodium channel activity (NAS)
0006814 sodium ion transport (NAS)

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schematic display of those terms with internal associations, click the node and browse the corresponding GO term
Domain Architecture (Details)
InterPro domains unassigned to SynO:
Members of this entry contain a region found exclusively in eukaryotic sodium channels or their subunits.any of which are voltage-gated. Members very often also contain between one and four copies of and.ess often.ne copy of .
  IPR010526:Sodium ion transport-associated
This group of proteins is found in sodium.otassium.nd calcium ion channels proteins. The proteins have 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some Na channels proteins the domain is repeated four times.hereas in others (e.g. K channels) the protein forms a tetramer in the membrane. A bacterial structure of the protein is known for the last two helices but is not included in the Pfam family due to it lacking the first four helices.
  IPR005821:Ion transport
Calmodulin (CaM) is recognized as a major calcium sensor and orchestrator of regulatory events through its interaction with a diverse group of cellular proteins. Three classes of recognition motifs exist for many of the known CaM binding proteins; the IQ motif as a consensus for Ca2+-independent binding and two related motifs for Ca2+-dependent binding.ermed18-14 and 1-5-10 based on the position of conserved hydrophobic residues .The regulatory domain of scallop myosin is a three-chain protein complex that switches on this motor in response to Ca2+ binding. Side-chain interactions link the two light chains in tandem to adjacent segments of the heavy chain bearing the IQ-sequence motif. The Ca2+-binding site is a novel EF-hand motif on the essential light chain and is stabilized by linkages involving the heavy chain and both light chains.ccounting for the requirement of all three chains for Ca2+ binding and regulation in the intact myosin molecule .
  IPR000048:IQ calmodulin-binding region
Voltage-dependent sodium channels are transmembrane (TM) proteinsresponsible for the depolarising phase of the action potential in mostelectrically excitable cells . They may exist in 3 states : theresting state.here the channel is closed; the activated state.here thechannel is open; and the inactivated state.here the channel is closedand refractory to opening. Several different structurally and functionallydistinct isoforms are found in mammals.oded for by a multigene family.hese being responsible for the different types of sodium ion currentsfound in excitable tissues.The structure of sodium channels is based on 4 internal repeats of a 6-helixbundle (in which 5 of the membrane-spanning segments are hydrophobic andthe other is positively charged).orming a 24-helical bundle. The chargedsegments are believed to be localised within clusters formed by their 5 hydrophobic neighbours: it is postulated that the charged domain may be thevoltage sensor region.ossibly moving outward on depolarisation.ausing aconformational change. This model.roposed by Noda et al. .ontrastswith that of Sato and Matsumoto .n which the TM segments are juxtaposedoctagonally. The basic structural motif (the 6-helix bundle) is also found in potassium and calcium channel alpha subunits.Cation channels are transport proteins responsible for the movement of cations through the membrane. These proteins contain 6 transmembrane helices in which the last two helices flank a loop which determines ion selectivity. In some sub-families (e.g. Na channels) the domain is repeated four times.hereas in others (e.g. K channels) the protein forms as a tetramer in the membrane.
  IPR001696:Na+ channel
Voltage-dependent sodium channels are transmembrane (TM) proteinsresponsible for the depolarising phase of the action potential in mostelectrically excitable cells . They may exist in 3 states : theresting state.here the channel is closed; the activated state.here thechannel is open; and the inactivated state.here the channel is closedand refractory to opening. Several different structurally and functionallydistinct isoforms are found in mammals.oded for by a multigene family.hese being responsible for the different types of sodium ion currentsfound in excitable tissues.The structure of sodium channels is based on 4 internal repeats of a 6-helixbundle (in which 5 of the membrane-spanning segments are hydrophobic andthe other is positively charged).orming a 24-helical bundle. The chargedsegments are believed to be localised within clusters formed by their 5 hydrophobic neighbours: it is postulated that the charged domain may be thevoltage sensor region.ossibly moving outward on depolarisation.ausing aconformational change. This model.roposed by Noda et al. .ontrastswith that of Sato and Matsumoto .n which the TM segments are juxtaposedoctagonally. The basic structural motif (the 6-helix bundle) is also found in potassium and calcium channel alpha subunits.The SCN1A gene encodes the NaB1 channel and is particularly expressed inthe brain.ut is also found in a variety of other tissues.anging from theretina to the olfactory bulb. Epilepsy. disorder of neuronalhyperexcitability.as been associated with altered kinetics of SCN1A.swell as delayed inactivation of SCN2A .
  IPR008051:Na+ channel 1
This domain consists of a duplication of two EF-hand units.here each unit is composed of two helices connected by a twelve-residue calcium-binding loop. The calcium ion in the EF-hand loop is coordinated in a pentagonal bipyramidal configuration. Many calcium-binding proteins contain an EF-hand type calcium-binding domain . These include: calbindin D9K.100 proteins such as calcyclin.olcalcin phl p 7 (a calcium-binding pollen allergen).steonectin.arvalbumin.almodulin family of proteins (troponin C.altractin.dc4p.yosin essential chain.alcineurin.ecoverin.eurocalcin).lasmodial-specific CaII-binding protein Cbp40.enta-EF-Hand proteins (sorcin.rancalcin.alpain).s well as multidomain proteins such as phosphoinositide-specific phospholipase C.ystrophin.b1 and alpha-actinin. The fold consists of four helices and an open array of two hairpins.
  IPR011992:EF-Hand type
IPR010526:Na_trans_assoc 
Evalue:-179.920822143555 
Location:1004-1228IPR005821:Ion_trans 
Evalue:-72 
Location:1254-1482IPR005821:Ion_trans 
Evalue:-71.2839965820313 
Location:156-422IPR005821:Ion_trans 
Evalue:-64.8239059448242 
Location:1575-1785IPR005821:Ion_trans 
Evalue:-61.2839965820313 
Location:802-991IPR000048:IQ 
Evalue:-2.37675070762634 
Location:1916-1936IPR011992:EF-Hand_type 
Evalue:0 
Location:1797-1838IPR008051:NACHANNEL1 
Evalue:0 
Location:1971-1989IPR008051:NACHANNEL1 
Evalue:0 
Location:1992-2009IPR000048:IQ 
Evalue:0 
Location:0-0
SequencesProtein: SCN1A_HUMAN (2009 aa)
mRNA: AB093548 NM_006920
Local Annotation
Synapse Ontology
A process that increases long-term neuronal synaptic plasticity, the ability of neuronal synapses to change long-term as circumstances require. Long-term neuronal synaptic plasticity generally involves increase or decrease in actual synapse numbers.
sdb:0039 positive regulation of long-term neuronal synaptic plasticity  (Evidence:keywords)
Na channel plays an important role in the course of action potential.
sdb:0287 Na channel  (Evidence:keywords)
KO assignmentK04833
  Level 3 annotation:
    sodium channel, voltage-gated, type I, alpha
  Level 2 annotation:
    Ion channels
Loci Structure (Details)Loci index, Chromosomal location, Length, Possible relational loci clusterExon1: 403 residues, 166555971-166557178Exon2: 92 residues, 166558901-166559172Exon3: 37 residues, 166560768-166560873Exon4: 48 residues, 166562793-166562931Exon5: 20 residues, 166564478-166564532Exon6: 96 residues, 166567227-166567509Exon7: 43 residues, 166574474-166574597Exon8: 60 residues, 166576864-166577038Exon9: 53 residues, 166578499-166578654Exon10: 42 residues, 166580362-166580483Exon11: 163 residues, 166600803-166601286Exon12: 121 residues, 166602531-166602888Exon13: 60 residues, 166604178-166604352Exon14: 81 residues, 166605986-166606225Exon15: 46 residues, 166607047-166607180Exon16: 118 residues, 166608457-166608805Exon17: 97 residues, 166609798-166610083Exon18: 71 residues, 166611525-166611732Exon19: 49 residues, 166612382-166612524Exon20: 23 residues, 166613641-166613705Exon21: 92 residues, 166616474-166616744Exon22: 32 residues, 166617607-166617699Exon23: 45 residues, 166619393-166619522Exon24: 31 residues, 166621166-166621254Exon25: 42 residues, 166623323-166623444Exon26: 90 residues, 166638113-166638377Exon27: 2 residues, -Jump to SCN1A_HUMANExon1: 393 residues, 166556000-166557178Exon2: 92 residues, 166558901-166559172Exon3: 37 residues, 166560768-166560873Exon4: 48 residues, 166562793-166562931Exon5: 20 residues, 166564478-166564532Exon6: 96 residues, 166567227-166567509Exon7: 43 residues, 166574474-166574597Exon8: 60 residues, 166576864-166577038Exon9: 53 residues, 166578499-166578654Exon10: 42 residues, 166580362-166580483Exon11: 163 residues, 166600803-166601286Exon12: 121 residues, 166602531-166602888Exon13: 60 residues, 166604178-166604352Exon14: 81 residues, 166605986-166606225Exon15: 46 residues, 166607047-166607180Exon16: 129 residues, 166608424-166608805Exon17: 97 residues, 166609798-166610083Exon18: 71 residues, 166611525-166611732Exon19: 49 residues, 166612382-166612524Exon20: 23 residues, 166613641-166613705Exon21: 92 residues, 166616474-166616744Exon22: 32 residues, 166617607-166617699Exon23: 45 residues, 166619393-166619522Exon24: 31 residues, 166621166-166621254Exon25: 42 residues, 166623323-166623444Exon26: 90 residues, 166638113-166638377Exon27: 2 residues, -Jump to SCN1A_HUMAN  
Tune and view alternative isoforms
Loci Cluster (Details)Loci: 4475 166763053-166876560 ~-114K 21504(SCN9A)(-)Loci: 4474 166555971-166638377 ~-82K 21501(SCN1A)(-)Link out to UCSC