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Protein

Sodium channel protein type 9 subunit alpha

Gene

SCN9A

Organism
Oryctolagus cuniculus (Rabbit)
Status
Reviewed-Annotation score: Annotation score: 4 out of 5-Experimental evidence at transcript leveli

Functioni

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. It is a tetrodotoxin-sensitive Na+ channel isoform. Plays a role in pain mechanisms, especially in the development of inflammatory pain.By similarity

GO - Molecular functioni

GO - Biological processi

Complete GO annotation...

Keywords - Molecular functioni

Ion channel, Sodium channel, Voltage-gated channel

Keywords - Biological processi

Ion transport, Sodium transport, Transport

Keywords - Ligandi

Sodium

Names & Taxonomyi

Protein namesi
Recommended name:
Sodium channel protein type 9 subunit alphaBy similarity
Alternative name(s):
Nas1 Publication
Schwann cell sodium channel
Sodium channel protein type IX subunit alpha
Voltage-gated sodium channel subunit alpha Nav1.7
Gene namesi
Name:SCN9ABy similarity
OrganismiOryctolagus cuniculus (Rabbit)
Taxonomic identifieri9986 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresLagomorphaLeporidaeOryctolagus
Proteomesi
  • UP000001811 Componenti: Unplaced

Subcellular locationi

  • Cell membrane By similarity; Multi-pass membrane protein By similarity
  • Cell projection By similarity

  • Note: In neurite terminals.By similarity

Topology

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Transmembranei122 – 14524Helical; Name=S1 of repeat ISequence analysisAdd
BLAST
Transmembranei154 – 17320Helical; Name=S2 of repeat ISequence analysisAdd
BLAST
Transmembranei187 – 20519Helical; Name=S3 of repeat ISequence analysisAdd
BLAST
Transmembranei212 – 23120Helical; Voltage-sensor; Name=S4 of repeat ISequence analysisAdd
BLAST
Transmembranei248 – 27124Helical; Name=S5 of repeat ISequence analysisAdd
BLAST
Transmembranei377 – 40226Helical; Name=S6 of repeat ISequence analysisAdd
BLAST
Transmembranei736 – 76025Helical; Name=S1 of repeat IISequence analysisAdd
BLAST
Transmembranei772 – 79524Helical; Name=S2 of repeat IISequence analysisAdd
BLAST
Transmembranei804 – 82320Helical; Name=S3 of repeat IISequence analysisAdd
BLAST
Transmembranei830 – 84920Helical; Voltage-sensor; Name=S4 of repeat IISequence analysisAdd
BLAST
Transmembranei866 – 88621Helical; Name=S5 of repeat IISequence analysisAdd
BLAST
Transmembranei940 – 96526Helical; Name=S6 of repeat IISequence analysisAdd
BLAST
Transmembranei1185 – 120824Helical; Name=S1 of repeat IIISequence analysisAdd
BLAST
Transmembranei1222 – 124726Helical; Name=S2 of repeat IIISequence analysisAdd
BLAST
Transmembranei1254 – 127522Helical; Name=S3 of repeat IIISequence analysisAdd
BLAST
Transmembranei1280 – 130122Helical; Voltage-sensor; Name=S4 of repeat IIISequence analysisAdd
BLAST
Transmembranei1321 – 134828Helical; Name=S5 of repeat IIISequence analysisAdd
BLAST
Transmembranei1428 – 145427Helical; Name=S6 of repeat IIISequence analysisAdd
BLAST
Transmembranei1508 – 153124Helical; Name=S1 of repeat IVSequence analysisAdd
BLAST
Transmembranei1543 – 156624Helical; Name=S2 of repeat IVSequence analysisAdd
BLAST
Transmembranei1573 – 159624Helical; Name=S3 of repeat IVSequence analysisAdd
BLAST
Transmembranei1607 – 162822Helical; Voltage-sensor; Name=S4 of repeat IVSequence analysisAdd
BLAST
Transmembranei1644 – 166623Helical; Name=S5 of repeat IVSequence analysisAdd
BLAST
Transmembranei1733 – 175725Helical; Name=S6 of repeat IVSequence analysisAdd
BLAST

GO - Cellular componenti

Complete GO annotation...

Keywords - Cellular componenti

Cell membrane, Cell projection, Membrane

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 19841984Sodium channel protein type 9 subunit alphaPRO_0000048504Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Glycosylationi209 – 2091N-linked (GlcNAc...)Sequence analysis
Glycosylationi281 – 2811N-linked (GlcNAc...)Sequence analysis
Glycosylationi1349 – 13491N-linked (GlcNAc...)Sequence analysis
Glycosylationi1363 – 13631N-linked (GlcNAc...)Sequence analysis
Glycosylationi1372 – 13721N-linked (GlcNAc...)Sequence analysis
Modified residuei1487 – 14871Phosphoserine; by PKCBy similarity

Post-translational modificationi

Phosphorylation at Ser-1487 by PKC in a highly conserved cytoplasmic loop increases peak sodium currents.By similarity
Ubiquitinated by NEDD4L; which may promote its endocytosis. Does not seem to be ubiquitinated by NEDD4.By similarity

Keywords - PTMi

Glycoprotein, Phosphoprotein, Ubl conjugation

Expressioni

Tissue specificityi

Expressed in the sciatic nerve, spinal cord, brainstem, cerebellum and cortex, but not expressed in the lung, skeletal and cardiac muscles, kidney and liver.1 Publication

Interactioni

Subunit structurei

The sodium channel complex consists of a large, channel-forming alpha subunit and 2-3 smaller, ancillary beta subunits (By similarity). Interacts with NEDD4 and NEDD4L (By similarity).By similarity

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000020201.

Structurei

3D structure databases

ProteinModelPortaliQ28644.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Repeati121 – 403283IAdd
BLAST
Repeati735 – 966232IIAdd
BLAST
Repeati1184 – 1455272IIIAdd
BLAST
Repeati1507 – 1758252IVAdd
BLAST
Domaini1886 – 191530IQAdd
BLAST

Domaini

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.By similarity

Sequence similaritiesi

Contains 1 IQ domain.Curated

Keywords - Domaini

Repeat, Transmembrane, Transmembrane helix

Phylogenomic databases

eggNOGiENOG410KCTY. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiQ28644.
KOiK04841.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF221. PTHR10037:SF221. 2 hits.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]

Sequences (2)i

Sequence statusi: Complete.

This entry describes 2 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 1 (identifier: Q28644-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MAMLPPPGPQ SFVRFTKQSL ALIEQRIAEG KTKEPKEEKK DDHDEGPKPS
60 70 80 90 100
SDLEAGKQLP FIYGDIPAGM VSEPLEDLDP YYADKKTFIV LNKGKAIFRF
110 120 130 140 150
NATPALYILS PFSPLRRISI KILVHSLFSM LIMCTILTNC IFMTMNNPAE
160 170 180 190 200
WTKNVEYTFT GIYTFESLVK IFARGFCVGE FTFLRDPWNW LDFIVIVFAY
210 220 230 240 250
LTEFVNLGNV SALRTFRVLR ALKTISVIPG LKTIVGALIQ SVKKLSDVII
260 270 280 290 300
LTVFCLSVFA LIGLQLFMGH LKHKCLRKIE NETLESIMSS IESEEDYKKY
310 320 330 340 350
FYYLEGSKDA LLCGFSTDSG QCPEGYYCVK AGRNPDYGYT SFDTFSWAFL
360 370 380 390 400
ALFRLMTQDY WENLYQQTLR AAGKTYMIFF VVVIFLGSFY LINLILAVVA
410 420 430 440 450
MAYEEQNQAN IEEAKQKELE FQQMLDRLKK EQEEAEAIAA AAAEYTSIGR
460 470 480 490 500
SRIMGLSESS SETSKLSSKS AKERRNRRKK KNQKKLSSGE EKGDDEKLSK
510 520 530 540 550
SESEESISRK QFHLGVEGHR LAREKRLSAP NQSPLSIRGS LFSARRSSRT
560 570 580 590 600
SLFSFKGRGK DIGSETEFAD DEHSIFGDNE SRRGSLFVPQ RPQERRSSNL
610 620 630 640 650
SQASRSPPML QMNGKMHSAV DCNGVVSLVD GPSALMLPNG QLLPEVIIDK
660 670 680 690 700
ATSDDSGTTQ IRKKRRSSSY LLSEDMLNDP HLRQRAMSRA SILTNTVEEL
710 720 730 740 750
EESRQKCPSW WYRFAHTFLI WNCSPFWIKF KKFIYIIVMD PFVDLAITIC
760 770 780 790 800
IVLNTLFMAM EHHPMTEEFK NVLVVGNLVF TGIFAAEMVL KLIAMDPYEY
810 820 830 840 850
FQVGWNVFDS LIVTLSLVEL FLADVEGLSV LRSFRLLRVF KLAKSWPTLN
860 870 880 890 900
MLIKIIGNSV GPLGNLTLVL AIIVFIFAVV GMQLFGKSYK ECVCKINDDC
910 920 930 940 950
SLPRWHMNDF FHSFLIVFRV LCGEWIETMW DCMEVAGQAM CLIVYMMVMV
960 970 980 990 1000
IGNLVVLNLF LALLLSSFSS DNLSAIEEDT DANNLQIAVT RIKKGINYVK
1010 1020 1030 1040 1050
QTLRELILKA FSKKPKISKE IRQAEDLNSK KENYISNRTL AEMSKDYNFH
1060 1070 1080 1090 1100
KEKDKISGFG SSMDKYLMEE SDHQSFIHNP SLTVTVPIAP GESDLENMNT
1110 1120 1130 1140 1150
EELSSDSESE YSKERLNRSS SSECSTVDNA LPGEGEEAEA EPVNSDEPEA
1160 1170 1180 1190 1200
CFTDGCVRRF PCCQVSIESG KGKIWWNIRK TCYRIVEHSW FESFIVLMIL
1210 1220 1230 1240 1250
LSSGALAFED IYIEKKKTIK IILEYADKIF TYIFILEMLL KWVAYGYKTY
1260 1270 1280 1290 1300
FTNAWCWLDF LIVDVSLVTL VANTLGYSDL GPIKSLRTLR ALRPLRALSR
1310 1320 1330 1340 1350
FEGMRVVVNA LIGAIPSIMN VLLVCLIFWL IFSIMGVNLF AGKFYQCVNT
1360 1370 1380 1390 1400
TDDSRFPTKQ VSNRSECFAL MNGSQNVRWK NLKVNFDNVG LRYLSLLQVA
1410 1420 1430 1440 1450
TFKGWMDIMY AAVDSVNVDQ QPSYEHNLYM YIYFVIFIIF GSFFTLNLFI
1460 1470 1480 1490 1500
GVIIDNFNQQ KKKLGGQDIF MTEEQKKYYN AMKKLGSKKP QKPIPRPGNK
1510 1520 1530 1540 1550
FQGCIFDLVT NQAFDITIMI LICLNMVTMM VEKEGQSDYM TDVLYWINVV
1560 1570 1580 1590 1600
FIILFTGECV LKLISLRHYY FTIGWNIFDF VVVILSIVGM FLAELIETYF
1610 1620 1630 1640 1650
VSPTLFRVIR LARIGRILRL IKGAKGIRTL LFALMMSLPA LFNIGLLLFL
1660 1670 1680 1690 1700
VMFIYAIFGM SNFAYVKKEA GINDMFNFET FGNSMICLFQ ITTSAGWDGL
1710 1720 1730 1740 1750
LAPILNSAPP DCDPKKVHPG SSTEGDCGSP SVGIFYFVSY IIISFLVVVN
1760 1770 1780 1790 1800
MYIAVILENF SVATEESTEP LSEDDFEMFY EVWEKFDPDA TQFIEYSKLS
1810 1820 1830 1840 1850
DFAAALDPPL LIAKPNKVQL IAMDLPMVSG DRIHCLDILF AFTKRVLGES
1860 1870 1880 1890 1900
GEMDSLRSQM EERFMSANPS KVSYEPITTT LKRKQEDVSA TVIQRAYRRY
1910 1920 1930 1940 1950
RLRQNVKNIS SIYIKEGDKD DDLPNKGDIV FDNVNSSSPE KTDATASTIS
1960 1970 1980
PPSYDSVTKP DKEKYEKDKT EKEDKGKDGK ETKK
Length:1,984
Mass (Da):225,751
Last modified:November 1, 1996 - v1
Checksum:i98F76860C9866AA0
GO
Isoform 2 (identifier: Q28644-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     200-229: YLTEFVNLGNVSALRTFRVLRALKTISVIP → YVTEFVDLGNVSALRTFRVLRALKTISVIP

Show »
Length:1,984
Mass (Da):225,738
Checksum:iA05CB05A33027C1C
GO

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei200 – 22930YLTEF…ISVIP → YVTEFVDLGNVSALRTFRVL RALKTISVIP in isoform 2. 1 PublicationVSP_012030Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U35238 mRNA. Translation: AAA89159.1.
RefSeqiNP_001075827.1. NM_001082358.1. [Q28644-1]
UniGeneiOcu.2049.

Genome annotation databases

GeneIDi100009210.
KEGGiocu:100009210.

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
U35238 mRNA. Translation: AAA89159.1.
RefSeqiNP_001075827.1. NM_001082358.1. [Q28644-1]
UniGeneiOcu.2049.

3D structure databases

ProteinModelPortaliQ28644.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9986.ENSOCUP00000020201.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi100009210.
KEGGiocu:100009210.

Organism-specific databases

CTDi6335.

Phylogenomic databases

eggNOGiENOG410KCTY. Eukaryota.
COG1226. LUCA.
HOGENOMiHOG000231755.
HOVERGENiHBG053100.
InParanoidiQ28644.
KOiK04841.

Family and domain databases

Gene3Di1.20.120.350. 4 hits.
InterProiIPR027359. Channel_four-helix_dom.
IPR005821. Ion_trans_dom.
IPR000048. IQ_motif_EF-hand-BS.
IPR001696. Na_channel_asu.
IPR010526. Na_trans_assoc.
IPR024583. Na_trans_cytopl.
IPR028803. SCN9A.
[Graphical view]
PANTHERiPTHR10037:SF221. PTHR10037:SF221. 2 hits.
PfamiPF00520. Ion_trans. 4 hits.
PF06512. Na_trans_assoc. 1 hit.
PF11933. Na_trans_cytopl. 1 hit.
[Graphical view]
PRINTSiPR00170. NACHANNEL.
SMARTiSM00015. IQ. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "Cloning of a sodium channel alpha subunit from rabbit Schwann cells."
    Belcher S.M., Zerillo C.A., Levenson R., Ritchie J.M., Howe J.R.
    Proc. Natl. Acad. Sci. U.S.A. 92:11034-11038(1995) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1 AND 2), TISSUE SPECIFICITY.
    Strain: New Zealand white.
    Tissue: Schwann cell.

Entry informationi

Entry nameiSCN9A_RABIT
AccessioniPrimary (citable) accession number: Q28644
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 23, 2004
Last sequence update: November 1, 1996
Last modified: May 11, 2016
This is version 97 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.