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P04774 (SCN1A_RAT) Reviewed, UniProtKB/Swiss-Prot

Last modified April 3, 2013. Version 117. Feed History...

Clusters with 100%, 90%, 50% identity | Documents (1) | Third-party data text xml rdf/xml gff fasta
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to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·DocumentsCustomize order

Names and origin

Protein namesRecommended name:
Sodium channel protein type 1 subunit alpha
Alternative name(s):
Sodium channel protein brain I subunit alpha
Sodium channel protein type I subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.1
Gene names
Name:Scn1a
OrganismRattus norvegicus (Rat) [Reference proteome]
Taxonomic identifier10116 [NCBI]
Taxonomic lineageEukaryota › Metazoa › Chordata › Craniata › Vertebrata › Euteleostomi › Mammalia › Eutheria › Euarchontoglires › Glires › Rodentia › Sciurognathi › Muroidea › Muridae › Murinae › Rattus

Protein attributes

Sequence length2009 AA.
Sequence statusComplete.
Protein existenceEvidence at transcript level

General annotation (Comments)

Function

Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na+ ions may pass in accordance with their electrochemical gradient.

Subunit structure

The sodium channel consists of a large polypeptide and 2-3 smaller ones. This sequence represents a large polypeptide. Interacts with FGF13; may regulate SCN1A activity By similarity.

Subcellular location

Membrane; Multi-pass membrane protein.

Domain

The sequence contains 4 internal repeats, each with 5 hydrophobic segments (S1,S2,S3,S5,S6) and one positively charged segment (S4). Segments S4 are probably the voltage-sensors and are characterized by a series of positively charged amino acids at every third position.

Sequence similarities

Belongs to the sodium channel (TC 1.A.1.10) family. Nav1.1/SCN1A subfamily. [View classification]

Contains 1 IQ domain.

Sequence annotation (Features)

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifier

Molecule processing

Chain1 – 20092009Sodium channel protein type 1 subunit alpha
PRO_0000048490

Regions

Transmembrane124 – 14724Helical; Name=S1 of repeat I
Transmembrane156 – 17520Helical; Name=S2 of repeat I
Transmembrane189 – 20719Helical; Name=S3 of repeat I
Transmembrane214 – 23320Helical; Voltage-sensor; Name=S4 of repeat I
Transmembrane250 – 27324Helical; Name=S5 of repeat I
Transmembrane400 – 42526Helical; Name=S6 of repeat I
Transmembrane763 – 78725Helical; Name=S1 of repeat II
Transmembrane799 – 82224Helical; Name=S2 of repeat II
Transmembrane831 – 85020Helical; Name=S3 of repeat II
Transmembrane857 – 87620Helical; Voltage-sensor; Name=S4 of repeat II
Transmembrane893 – 91321Helical; Name=S5 of repeat II
Transmembrane967 – 99226Helical; Name=S6 of repeat II
Transmembrane1214 – 123724Helical; Name=S1 of repeat III
Transmembrane1251 – 127626Helical; Name=S2 of repeat III
Transmembrane1283 – 130422Helical; Name=S3 of repeat III
Transmembrane1309 – 133022Helical; Voltage-sensor; Name=S4 of repeat III
Transmembrane1350 – 137728Helical; Name=S5 of repeat III
Transmembrane1457 – 148327Helical; Name=S6 of repeat III
Transmembrane1537 – 156024Helical; Name=S1 of repeat IV
Transmembrane1572 – 159524Helical; Name=S2 of repeat IV
Transmembrane1602 – 162524Helical; Name=S3 of repeat IV
Transmembrane1636 – 165722Helical; Voltage-sensor; Name=S4 of repeat IV
Transmembrane1673 – 169523Helical; Name=S5 of repeat IV
Transmembrane1762 – 178625Helical; Name=S6 of repeat IV
Repeat110 – 454345I
Repeat750 – 1022273II
Repeat1200 – 1514315III
Repeat1523 – 1821299IV
Domain1915 – 194430IQ

Amino acid modifications

Glycosylation2111N-linked (GlcNAc...) Potential
Glycosylation2841N-linked (GlcNAc...) Potential
Glycosylation2951N-linked (GlcNAc...) Potential
Glycosylation3011N-linked (GlcNAc...) Potential
Glycosylation3061N-linked (GlcNAc...) Potential
Glycosylation3381N-linked (GlcNAc...) Potential
Glycosylation6011N-linked (GlcNAc...) Potential
Glycosylation6211N-linked (GlcNAc...) Potential
Glycosylation6811N-linked (GlcNAc...) Potential
Glycosylation8921N-linked (GlcNAc...) Potential
Glycosylation10601N-linked (GlcNAc...) Potential
Glycosylation10641N-linked (GlcNAc...) Potential
Glycosylation10801N-linked (GlcNAc...) Potential
Glycosylation11461N-linked (GlcNAc...) Potential
Glycosylation13781N-linked (GlcNAc...) Potential
Glycosylation13921N-linked (GlcNAc...) Potential
Glycosylation14031N-linked (GlcNAc...) Potential

Sequences

Sequence LengthMass (Da)Tools
P04774 [UniParc].

Last modified August 13, 1987. Version 1.
Checksum: 6808466F6368373B

FASTA2,009228,770
        10         20         30         40         50         60 
MEQTVLVPPG PDSFNFFTRE SLAAIERRIA EEKAKNPKPD KKDDDENGPK PNSDLEAGKN 

        70         80         90        100        110        120 
LPFIYGDIPP EMVSEPLEDL DPYYINKKTF IVLNKGKAIF RFSATSALYI LTPFNPLRKI 

       130        140        150        160        170        180 
AIKILVHSLF SMLIMCTILT NCVFMTMSNP PDWTKNVEYT FTGIYTFESL IKIIARGFCL 

       190        200        210        220        230        240 
EDFTFLRDPW NWLDFTVITF AYVTEFVDLG NVSALRTFRV LRALKTISVI PGLKTIVGAL 

       250        260        270        280        290        300 
IQSVKKLSDV MILTVFCLSV FALIGLQLFM GNLRNKCVQW PPTNASLEEH SIEKNVTTDY 

       310        320        330        340        350        360 
NGTLVNETVF EFDWKSYIQD SRYHYFLEGV LDALLCGNSS DAGQCPEGYM CVKAGRNPNY 

       370        380        390        400        410        420 
GYTSFDTFSW AFLSLFRLMT QDFWENLYQL TLRAAGKTYM IFFVLVIFLG SFYLINLILA 

       430        440        450        460        470        480 
VVAMAYEEQN QATLEEAEQK EAEFQQMLEQ LKKQQEAAQQ AAAATASEHS REPSAAGRLS 

       490        500        510        520        530        540 
DSSSEASKLS SKSAKERRNR RKKRKQKEQS GGEEKDDDEF HKSESEDSIR RKGFRFSIEG 

       550        560        570        580        590        600 
NRLTYEKRYS SPHQSLLSIR GSLFSPRRNS RTSLFSFRGR AKDVGSENDF ADDEHSTFED 

       610        620        630        640        650        660 
NESRRDSLFV PRRHGERRNS NLSQTSRSSR MLAGLPANGK MHSTVDCNGV VSLVGGPSVP 

       670        680        690        700        710        720 
TSPVGQLLPE VIIDKPATDD NGTTTETEMR KRRSSSFHVS MDFLEDPSQR QRAMSIASIL 

       730        740        750        760        770        780 
TNTVEELEES RQKCPPCWYK FSNIFLIWDC SPYWLKVKHI VNLVVMDPFV DLAITICIVL 

       790        800        810        820        830        840 
NTLFMAMEHY PMTEHFNHVL TVGNLVFTGI FTAEMFLKII AMDPYYYFQE GWNIFDGFIV 

       850        860        870        880        890        900 
TLSLVELGLA NVEGLSVLRS FRLLRVFKLA KSWPTLNMLI KIIGNSVGAL GNLTLVLAII 

       910        920        930        940        950        960 
VFIFAVVGMQ LFGKSYKDCV CKIATDCKLP RWHMNDFFHS FLIVFRVLCG EWIETMWDCM 

       970        980        990       1000       1010       1020 
EVAGQAMCLT VFMMVMVIRN LVVLNLFLAL LLSSFSADNL AATDDDNEMN NLQIAVDRMH 

      1030       1040       1050       1060       1070       1080 
KGVAYVKRKI YEFIQQSFVR KQKILDEIKP LDDLNNRKDN CTSNHTTEIG KDLDCLKDVN 

      1090       1100       1110       1120       1130       1140 
GTTSGIGTGS SVEKYIIDES DYMSFINNPS LTVTVPIAVG ESDFENLNTE DFSSESDLEE 

      1150       1160       1170       1180       1190       1200 
SKEKLNESSS SSEGSTVDIG APAEEQPVME PEETLEPEAC FTEGCVQRFK CCQISVEEGR 

      1210       1220       1230       1240       1250       1260 
GKQWWNLRRT CFRIVEHNWF ETFIVFMILL SSGALAFEDI YIDQRKTIKT MLEYADKVFT 

      1270       1280       1290       1300       1310       1320 
YIFILEMLLK WVAYGYQTYF TNAWCWLDFL IVDVSLVSLT ANALGYSELG AIKSLRTLRA 

      1330       1340       1350       1360       1370       1380 
LRPLRALSRF EGMRVVVNAL LGAIPSIMNV LLVCLIFWLI FSIMGVNLFA GKFYHCVNTT 

      1390       1400       1410       1420       1430       1440 
TGDTFEITEV NNHSDCLKLI ERNETARWKN VKVNFDNVGF GYLSLLQVAT FKGWMDIMYA 

      1450       1460       1470       1480       1490       1500 
AVDSRNVELQ PKYEESLYMY LYFVIFIIFG SFFTLNLFIG VIIDNFNQQK KKFGGQDIFM 

      1510       1520       1530       1540       1550       1560 
TEEQKKYYNA MKKLGSKKPQ KPIPRPGNKF QGMVFDFVTR QVFDISIMIL ICLNMVTMMV 

      1570       1580       1590       1600       1610       1620 
ETDDQSDYVT SILSRINLVF IVLFTGECVL KLISLRHYYF TIGWNIFDFV VVILSIVGMF 

      1630       1640       1650       1660       1670       1680 
LAELIEKYFV SPTLFRVIRL ARIGRILRLI KGAKGIRTLL FALMMSLPAL FNIGLLLFLV 

      1690       1700       1710       1720       1730       1740 
MFIYAIFGMS NFAYVKREVG IDDMFNFETF GNSMICLFQI TTSAGWDGLL APILNSKPPD 

      1750       1760       1770       1780       1790       1800 
CDPNKVNPGS SVKGDCGNPS VGIFFFVSYI IISFLVVVNM YIAVILENFS VATEESAEPL 

      1810       1820       1830       1840       1850       1860 
SEDDFEMFYE VWEKFDPDAT QFMEFEKLSQ FAAALEPPLN LPQPNKLQLI AMDLPMVSGD 

      1870       1880       1890       1900       1910       1920 
RIHCLDILFA FTKRVLGESG EMDALRIQME ERFMASNPSK VSYQPITTTL KRKQEEVSAV 

      1930       1940       1950       1960       1970       1980 
IIQRAYRRHL LKRTVKQASF TYNKNKLKGG ANLLVKEDMI IDRINENSIT EKTDLTMSTA 

      1990       2000 
ACPPSYDRVT KPIVEKHEQE GKDEKAKGK

« Hide

References

[1]"Existence of distinct sodium channel messenger RNAs in rat brain."
Noda M., Ikeda T., Kayano T., Suzuki H., Takeshima H., Kurasaki M., Takahashi H., Numa S.
Nature 320:188-192(1986) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[2]"Structure and function of sodium channel."
Noda M., Numa S.
J. Recept. Res. 7:467-497(1987) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA].
[3]"Developmentally regulated alternative RNA splicing of rat brain sodium channel mRNAs."
Sarao R., Gupta S.K., Auld V.J., Dunn R.J.
Nucleic Acids Res. 19:5673-5679(1991) [PubMed] [Europe PMC] [Abstract]
Cited for: NUCLEOTIDE SEQUENCE [MRNA] OF 177-253.
Strain: Sprague-Dawley.
Tissue: Brain.
+Additional computationally mapped references.

Cross-references

Sequence databases

EMBL
GenBank
DDBJ		X03638 mRNA. Translation: CAA27286.1.
M22253 mRNA. Translation: AAA79965.1.
IPIIPI00198841.
PIRA25019.
RefSeqNP_110502.1. NM_030875.1.
UniGeneRn.32079.

3D structure databases

ProteinModelPortalP04774.
ModBaseSearch...

Protein-protein interaction databases

STRING10116.ENSRNOP00000051071.

Proteomic databases

PaxDbP04774.
PRIDEP04774.

Protocols and materials databases

StructuralBiologyKnowledgebaseSearch...

Genome annotation databases

GeneID81574.
KEGGrno:81574.
UCSCRGD:69364. rat.

Organism-specific databases

CTD6323.
RGD69364. Scn1a.

Phylogenomic databases

eggNOGCOG1226.
HOGENOMHOG000231755.
HOVERGENHBG053100.
KOK04833.
OrthoDBEOG4Z36CT.

Gene expression databases

ArrayExpressP04774.
GenevestigatorP04774.

Family and domain databases

InterProIPR024583. DUF3451.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR008051. Na_channel_a1su.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
[Graphical view]
PfamPF11933. DUF3451. 1 hit.
PF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
[Graphical view]
PRINTSPR00170. NACHANNEL.
PR01664. NACHANNEL1.
SMARTSM00015. IQ. 1 hit.
[Graphical view]
PROSITEPS50096. IQ. False negative.
[Graphical view]
ProtoNetSearch...

Other

BindingDBP04774.
ChEMBLCHEMBL4906.
NextBio615093.

Entry information

Entry nameSCN1A_RAT
AccessionPrimary (citable) accession number: P04774
Entry history
Integrated into UniProtKB/Swiss-Prot: August 13, 1987
Last sequence update: August 13, 1987
Last modified: April 3, 2013
This is version 117 of the entry and version 1 of the sequence. [Complete history]
Entry statusReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Relevant documents

SIMILARITY comments

Index of protein domains and families

to top of pageNames·Attributes·General annotation·Ontologies·Sequence annotation·Sequences·References·Cross-refs·Entry info·Documents