Scn5a (sodium voltage-gated channel alpha subunit 5) - Rat Genome Database

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Gene: Scn5a (sodium voltage-gated channel alpha subunit 5) Rattus norvegicus
Analyze
Symbol: Scn5a
Name: sodium voltage-gated channel alpha subunit 5
RGD ID: 3637
Description: Enables ankyrin binding activity; fibroblast growth factor binding activity; and voltage-gated sodium channel activity involved in cardiac muscle cell action potential. Involved in several processes, including brain development; response to denervation involved in regulation of muscle adaptation; and sodium ion import across plasma membrane. Located in T-tubule and intercalated disc. Biomarker of brain ischemia and congestive heart failure. Human ortholog(s) of this gene implicated in heart conduction disease (multiple); intrinsic cardiomyopathy (multiple); and sudden infant death syndrome. Orthologous to human SCN5A (sodium voltage-gated channel alpha subunit 5); PARTICIPATES IN acebutolol pharmacodynamics pathway; adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway; amiodarone pharmacodynamics pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Nav1.5; RATRSKM2X; rSkM2; RSKM2X; SCAL; Scn2x; skeletal muscle voltage-sensitive sodium channel subtype 2; sodium channel protein cardiac muscle subunit alpha; sodium channel protein type 5 subunit alpha; sodium channel protein type V subunit alpha; sodium channel, voltage-gated, type 5, alpha subunit; sodium channel, voltage-gated, type V, alpha; sodium channel, voltage-gated, type V, alpha polypeptide; sodium channel, voltage-gated, type V, alpha subunit; voltage-gated sodium channel Nav1.5c; voltage-gated sodium channel subunit alpha Nav1.5
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Scn5aem2Mcwi  
Genetic Models: DA-Scn5aem2Mcwi
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,220,905 - 119,318,816 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,220,905 - 119,318,769 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8124,802,735 - 124,900,397 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08123,001,756 - 123,099,420 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08120,835,478 - 120,933,167 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08128,169,191 - 128,266,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,169,191 - 128,266,639 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,375,781 - 127,471,879 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,446,479 - 124,545,301 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18124,467,115 - 124,565,038 (-)NCBI
Celera8118,371,960 - 118,468,948 (-)NCBICelera
RH 3.4 Map81282.5RGD
Cytogenetic Map8q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
arrhythmogenic right ventricular cardiomyopathy  (ISO)
atrial fibrillation  (ISO)
atrial standstill 1  (ISO)
atrioventricular block  (ISO)
brain ischemia  (IEP)
Brugada syndrome  (ISO)
Brugada syndrome 1  (ISO,ISS)
cardiac arrest  (ISO)
Cardiac Arrhythmias  (ISO)
Cardiac Conduction Defect  (ISO)
Cardiac Conduction Defect, Nonprogressive  (ISO)
Cardiac Conduction Defect, Nonspecific  (ISO)
cardiomyopathy  (ISO)
catecholaminergic polymorphic ventricular tachycardia  (ISO)
catecholaminergic polymorphic ventricular tachycardia 1  (ISO)
congestive heart failure  (IEP)
Death  (ISO)
dilated cardiomyopathy  (ISO)
dilated cardiomyopathy 1A  (ISO)
dilated cardiomyopathy 1B  (ISO)
dilated cardiomyopathy 1E  (ISO)
dilated cardiomyopathy 1H  (ISO)
Dilated Cardiomyopathy with Left Ventricular Noncompaction  (ISO)
Familial Atrial Fibrillation 10  (ISO)
familial hypertrophic cardiomyopathy  (ISO)
fetal akinesia deformation sequence syndrome 1  (ISO)
genetic disease  (ISO)
Heart Block  (ISO)
heart conduction disease  (ISO)
hemiplegia  (ISO)
hereditary sensory and autonomic neuropathy type 7  (ISO)
hypertrophic cardiomyopathy  (ISO)
hypertrophic cardiomyopathy 1  (ISO)
Immunodeficiency 68  (ISO)
Infant Death  (ISO)
left ventricular noncompaction  (ISO)
Left Ventricular Noncompaction 1  (ISO)
long QT syndrome  (ISO)
long QT syndrome 1  (ISO)
long QT syndrome 2  (ISO)
Long QT Syndrome 2/3  (ISO)
long QT syndrome 3  (ISO,ISS)
Long QT Syndrome 3/6  (ISO)
migraine  (ISO)
Nonprogressive Heart Block  (ISO)
Paroxysmal Ventricular Fibrillation  (ISO)
progressive familial heart block  (ISO)
Progressive Familial Heart Block Type I  (ISO)
progressive familial heart block type IA  (ISO,ISS)
Romano-Ward Syndrome  (ISO)
sick sinus syndrome  (ISO,ISS)
Sick Sinus Syndrome 1, Autosomal Recessive  (ISO)
Sudden Cardiac Death  (ISO)
Sudden Death  (ISO)
sudden infant death syndrome  (ISO)
Sudden Unexpected Nocturnal Death Syndrome  (ISO)
Syncope  (ISO)
Torsades de Pointes  (ISO)
Ventricular Fibrillation  (ISO)
Ventricular Fibrillation, Paroxysmal Familial, 1  (ISO)
Ventricular Tachycardia  (ISO)
Visceral Heterotaxy 4, Autosomal  (ISO)
Wolff-Parkinson-White syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,2-dimethylhydrazine  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3,3',5,5'-tetrabromobisphenol A  (ISO)
4,4'-sulfonyldiphenol  (EXP,ISO)
4-amino-5-chloro-N-[1-[3-(4-fluorophenoxy)propyl]-3-methoxy-4-piperidinyl]-2-methoxybenzamide  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
9-phenanthrol  (ISO)
Aflatoxin B2 alpha  (ISO)
ajmaline  (ISO)
all-trans-retinoic acid  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
atrazine  (EXP)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (EXP)
brompheniramine  (ISO)
butanal  (ISO)
cannabidiol  (ISO)
chloroform  (ISO)
choline  (ISO)
cisapride  (ISO)
crizotinib  (ISO)
crocidolite asbestos  (ISO)
Cuprizon  (EXP)
daunorubicin  (ISO)
diclofenac  (ISO)
doxorubicin  (EXP,ISO)
endosulfan  (EXP)
ethanol  (ISO)
ezogabine  (ISO)
flecainide  (ISO)
fluorescein 5-isothiocyanate  (ISO)
fluvoxamine  (ISO)
folic acid  (ISO)
furan  (EXP)
gentamycin  (EXP)
ibogaine  (ISO)
icajine  (ISO)
isoprenaline  (EXP)
L-methionine  (ISO)
lidocaine  (ISO)
limonene  (ISO)
lithium chloride  (ISO)
manganese(II) chloride  (EXP)
meloxicam  (ISO)
methamphetamine  (EXP,ISO)
methoxychlor  (EXP)
mexiletine  (ISO)
mitoxantrone  (ISO)
N,N-diethyl-m-toluamide  (EXP)
nefazodone  (ISO)
nifedipine  (EXP)
nimesulide  (ISO)
ozone  (ISO)
paracetamol  (EXP)
paraquat  (EXP)
pentanal  (ISO)
permethrin  (EXP)
piroxicam  (ISO)
quercetin  (ISO)
quinidine  (ISO)
ranolazine  (ISO)
resveratrol  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sodium atom  (EXP)
strychnine  (ISO)
sulforaphane  (ISO)
sunitinib  (ISO)
telmisartan  (ISO)
tetrodotoxin  (EXP)
titanium dioxide  (ISO)
tributylstannane  (EXP)
triptonide  (ISO)
tris(2-butoxyethyl) phosphate  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
action potential  (IEA)
atrial cardiac muscle cell action potential  (ISO,ISS)
AV node cell action potential  (ISO,ISS)
AV node cell to bundle of His cell communication  (ISO,ISS)
brainstem development  (IEP)
bundle of His cell action potential  (ISO,ISS)
calcium ion homeostasis  (ISO)
cardiac muscle cell action potential involved in contraction  (ISO,ISS)
cardiac muscle contraction  (ISO,ISS)
cardiac ventricle development  (ISO)
cell communication involved in cardiac conduction  (ISO)
cellular response to calcium ion  (IEA,ISO,ISS)
cerebellum development  (IEP)
establishment of localization in cell  (ISO)
membrane depolarization  (ISO,ISS)
membrane depolarization during action potential  (IBA,ISO,ISS)
membrane depolarization during atrial cardiac muscle cell action potential  (IEA,ISO)
membrane depolarization during AV node cell action potential  (IEA,ISO,ISS)
membrane depolarization during bundle of His cell action potential  (IEA,ISO,ISS)
membrane depolarization during cardiac muscle cell action potential  (IMP,ISO,ISS)
membrane depolarization during Purkinje myocyte cell action potential  (IEA,ISO,ISS)
membrane depolarization during SA node cell action potential  (IEA,ISO,ISS)
muscle cell cellular homeostasis  (ISO)
neuronal action potential  (IBA)
odontogenesis of dentin-containing tooth  (IEP)
positive regulation of action potential  (IMP)
positive regulation of epithelial cell proliferation  (IMP)
positive regulation of heart rate  (IMP)
positive regulation of sodium ion transport  (IEA,ISO,ISS)
regulation of atrial cardiac muscle cell membrane depolarization  (IBA,IEA,ISO,ISS)
regulation of atrial cardiac muscle cell membrane repolarization  (IEA,ISO,ISS)
regulation of cardiac muscle cell contraction  (IEA,ISO,ISS)
regulation of heart rate  (IBA,ISO,ISS)
regulation of heart rate by cardiac conduction  (IEA,ISO,ISS)
regulation of monoatomic ion transmembrane transport  (IEA)
regulation of sodium ion transmembrane transport  (IEA,ISO,ISS)
regulation of ventricular cardiac muscle cell membrane depolarization  (IEA,ISO,ISS)
regulation of ventricular cardiac muscle cell membrane repolarization  (IEA,ISO,ISS)
response to denervation involved in regulation of muscle adaptation  (IMP)
response to organic cyclic compound  (ISO)
SA node cell action potential  (ISO,ISS)
sodium ion import across plasma membrane  (IMP,ISO)
sodium ion transmembrane transport  (IBA,IEA,IMP,ISO,ISS)
sodium ion transport  (ISO,ISS)
telencephalon development  (IEP)
ventricular cardiac muscle cell action potential  (IEA,ISO)

Cellular Component
axon  (IBA)
caveola  (IEA,ISO,ISS)
cell surface  (IEA,ISO)
endoplasmic reticulum  (IEA,ISO,ISS)
intercalated disc  (IDA,IEA,ISO,ISS)
lateral plasma membrane  (ISO)
membrane  (ISO,ISS)
nucleolus  (IEA,ISO)
nucleoplasm  (IEA,ISO)
perinuclear region of cytoplasm  (IEA)
plasma membrane  (ISO)
sarcolemma  (ISO)
sodium channel complex  (ISO)
T-tubule  (IDA,IEA,ISO)
voltage-gated sodium channel complex  (IBA,IEA,ISO,ISS)
Z disc  (IEA,ISO,ISS)

Molecular Pathway Annotations     Click to see Annotation Detail View
acebutolol pharmacodynamics pathway  (ISO)
adrenergic beta receptor agonist and beta-blocker pharmacodynamics pathway  (ISO)
amiodarone pharmacodynamics pathway  (ISO)
amlodipine pharmacodynamics pathway  (ISO)
atenolol pharmacodynamics pathway  (ISO)
betaxolol pharmacodynamics pathway  (ISO)
bisoprolol pharmacodynamics pathway  (ISO)
bupranolol drug pathway  (ISO)
bupranolol pharmacodynamics pathway  (ISO)
calcium/calmodulin dependent kinase 2 signaling pathway  (ISO)
carvedilol pharmacodynamics pathway  (ISO)
diltiazem pharmacodynamics pathway  (ISO)
disopyramide pharmacodynamics pathway  (ISO)
dobutamine pharmacodynamics pathway  (ISO)
esmolol pharmacodynamics pathway  (ISO)
flecainde pharmacodynamics pathway  (ISO)
fosphenytoin pharmacodynamics pathway  (ISO)
fosphenytoin pharmacokinetics pathway  (ISO)
ibutilide pharmacodynamics pathway  (ISO)
isoprenaline pharmacodynamics pathway  (ISO)
isradipine pharmacodynamics pathway  (ISO)
levobunolol pharmacodynamics pathway  (ISO)
lidocaine pharmacodynamics pathway  (ISO)
metoprolol pharmacodynamics pathway  (ISO)
mexiletine pharmacodynamics pathway  (ISO)
nadolol pharmacodynamics pathway  (ISO)
nebivolol pharmacodynamics pathway  (ISO)
nifedipine pharmacodynamics pathway  (ISO)
nimodipine pharmacodynamics pathway  (ISO)
nisoldipine pharmacodynamics pathway  (ISO)
nitrendipine pharmacodynamics pathway  (ISO)
penbutolol pharmacodynamics pathway  (ISO)
phenytoin pharmacodynamics pathway  (ISO)
pindolol pharmacodynamics pathway  (ISO)
procainamide pharmacodynamics pathway  (ISO)
propranolol pharmacodynamics pathway  (ISO)
quinidine pharmacodynamics pathway  (ISO)
sotalol pharmacodynamics pathway  (ISO)
timolol pharmacodynamics pathway  (ISO)
verapamil pharmacodynamics pathway  (ISO)

References

References - curated
# Reference Title Reference Citation
1. Expression and intracellular localization of an SCN5A double mutant R1232W/T1620M implicated in Brugada syndrome. Baroudi G, etal., Circ Res 2002 Jan 11;90(1):E11-6.
2. Odontoblasts in developing, mature and ageing rat teeth have multiple phenotypes that variably express all nine voltage-gated sodium channels. Byers MR and Westenbroek RE, Arch Oral Biol. 2011 Nov;56(11):1199-220.
3. Characterization of sodium channel alpha- and beta-subunits in rat and mouse cardiac myocytes. Dhar Malhotra J, etal., Circulation. 2001 Mar 6;103(9):1303-10.
4. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
6. [Expression and function of voltage-gated Na+ channel isoforms in rat sinoatrial node]. Huang X, etal., Nan Fang Yi Ke Da Xue Xue Bao. 2007 Jan;27(1):52-5.
7. High-density rat radiation hybrid maps containing over 24,000 SSLPs, genes, and ESTs provide a direct link to the rat genome sequence. Kwitek AE, etal., Genome Res. 2004 Apr;14(4):750-7
8. Modulation of the cardiac sodium channel Nav1.5 by fibroblast growth factor homologous factor 1B. Liu CJ, etal., J Biol Chem. 2003 Jan 10;278(2):1029-36. Epub 2002 Oct 24.
9. Voltage-gated Nav channel targeting in the heart requires an ankyrin-G dependent cellular pathway. Lowe JS, etal., J Cell Biol. 2008 Jan 14;180(1):173-86. Epub 2008 Jan 7.
10. Drug-induced long-QT syndrome associated with a subclinical SCN5A mutation. Makita N, etal., Circulation 2002 Sep 3;106(10):1269-74.
11. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
12. Nav1.5 E1053K mutation causing Brugada syndrome blocks binding to ankyrin-G and expression of Nav1.5 on the surface of cardiomyocytes. Mohler PJ, etal., Proc Natl Acad Sci U S A. 2004 Dec 14;101(50):17533-8. Epub 2004 Dec 3.
13. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
14. Remodeling of the cardiac sodium channel, connexin43, and plakoglobin at the intercalated disk in patients with arrhythmogenic cardiomyopathy. Noorman M, etal., Heart Rhythm. 2013 Mar;10(3):412-9. doi: 10.1016/j.hrthm.2012.11.018. Epub 2012 Nov 23.
15. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
16. SMPDB Annotation Import Pipeline Pipeline to import SMPDB annotations from SMPDB into RGD
17. Cloning and expression of the two new variants of Nav1.5/SCN5A in rat brain. Ren CT, etal., Mol Cell Biochem. 2012 Jun;365(1-2):139-48. Epub 2012 Feb 14.
18. GOA pipeline RGD automated data pipeline
19. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
20. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
21. Molecular cloning of a putative tetrodotoxin-resistant rat heart Na+ channel isoform. Rogart RB, etal., Proc Natl Acad Sci U S A 1989 Oct;86(20):8170-4.
22. New therapeutic targets in cardiology: arrhythmias and Ca2+/calmodulin-dependent kinase II (CaMKII). Rokita AG and Anderson ME, Circulation. 2012 Oct 23;126(17):2125-39. doi: 10.1161/CIRCULATIONAHA.112.124990.
23. Loss of plakophilin-2 expression leads to decreased sodium current and slower conduction velocity in cultured cardiac myocytes. Sato PY, etal., Circ Res. 2009 Sep 11;105(6):523-6. Epub 2009 Aug 6.
24. Fibrillation potentials of denervated rat skeletal muscle are associated with expression of cardiac-type voltage-gated sodium channel isoform Nav1.5. Sekiguchi K, etal., Clin Neurophysiol. 2012 Feb 13.
25. An antisense oligonucleotide against H1 inhibits the classical sodium current but not ICa(TTX) in rat ventricular cells. Sha Q, etal., J Physiol. 2003 Mar 1;547(Pt 2):435-40. Epub 2003 Jan 24.
26. Compendium of cardiac channel mutations in 541 consecutive unrelated patients referred for long QT syndrome genetic testing. Tester DJ, etal., Heart Rhythm. 2005 May;2(5):507-17.
27. Ionic mechanisms underlying action potential prolongation by focal cerebral ischemia in rat ventricular myocytes. Wang L, etal., Cell Physiol Biochem. 2009;23(4-6):305-16. Epub 2009 May 6.
28. Involvement of Kv1.1 and Nav1.5 in proliferation of gastric epithelial cells. Wu WK, etal., J Cell Physiol. 2006 May;207(2):437-44.
29. Increased late sodium currents are related to transcription of neuronal isoforms in a pressure-overload model. Xi Y, etal., Eur J Heart Fail. 2009 Aug;11(8):749-57. Epub 2009 Jul 7.
30. A common variant alters SCN5A-miR-24 interaction and associates with heart failure mortality. Zhang X, etal., J Clin Invest. 2018 Mar 1;128(3):1154-1163. doi: 10.1172/JCI95710. Epub 2018 Feb 19.
31. Predicting Patient Response to the Antiarrhythmic Mexiletine Based on Genetic Variation: Personalized Medicine for Long QT Syndrome. Zhu W, etal., Circ Res. 2018 Dec 18. doi: 10.1161/CIRCRESAHA.118.314050.
Additional References at PubMed
PMID:7889574   PMID:8286044   PMID:8889548   PMID:10471492   PMID:11834499   PMID:11972032   PMID:14500339   PMID:15047701   PMID:15217910   PMID:15272007   PMID:15746173   PMID:15809371  
PMID:15932895   PMID:16115203   PMID:16172272   PMID:16728661   PMID:16966585   PMID:17060380   PMID:17592081   PMID:17884088   PMID:17900547   PMID:18032528   PMID:18065446   PMID:18178574  
PMID:18184654   PMID:18591664   PMID:18616619   PMID:19074138   PMID:19167345   PMID:19376164   PMID:19666841   PMID:19745168   PMID:19808477   PMID:19943616   PMID:20042427   PMID:20517693  
PMID:20724705   PMID:20877009   PMID:21051419   PMID:21164104   PMID:21167176   PMID:21677263   PMID:21817159   PMID:21895525   PMID:22247482   PMID:22514276   PMID:22529811   PMID:22766342  
PMID:22811280   PMID:23085483   PMID:23420830   PMID:23684688   PMID:24998131   PMID:25850710   PMID:26059563   PMID:26067667   PMID:26187182   PMID:26279430   PMID:26392562   PMID:26459913  
PMID:26786162   PMID:27861438   PMID:28205593   PMID:29184507   PMID:29393394   PMID:29514831   PMID:30506890   PMID:30772377   PMID:30860472   PMID:32046907   PMID:33145656   PMID:33397917  
PMID:33803193   PMID:34520724   PMID:35384053  


Genomics

Comparative Map Data
Scn5a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.28119,220,905 - 119,318,816 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8119,220,905 - 119,318,769 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8124,802,735 - 124,900,397 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08123,001,756 - 123,099,420 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08120,835,478 - 120,933,167 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08128,169,191 - 128,266,681 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8128,169,191 - 128,266,639 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08127,375,781 - 127,471,879 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48124,446,479 - 124,545,301 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18124,467,115 - 124,565,038 (-)NCBI
Celera8118,371,960 - 118,468,948 (-)NCBICelera
RH 3.4 Map81282.5RGD
Cytogenetic Map8q32NCBI
SCN5A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38338,548,062 - 38,649,687 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl338,548,057 - 38,649,687 (-)EnsemblGRCh38hg38GRCh38
GRCh37338,589,553 - 38,691,178 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36338,564,557 - 38,666,167 (-)NCBINCBI36Build 36hg18NCBI36
Build 34338,564,557 - 38,666,167NCBI
Cytogenetic Map3p22.2NCBI
HuRef338,631,798 - 38,733,467 (-)NCBIHuRef
CHM1_1338,541,190 - 38,642,759 (-)NCBICHM1_1
T2T-CHM13v2.0338,554,106 - 38,661,891 (-)NCBIT2T-CHM13v2.0
Scn5a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399119,312,470 - 119,408,096 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9119,312,474 - 119,408,082 (-)EnsemblGRCm39 Ensembl
GRCm389119,483,404 - 119,579,030 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9119,483,408 - 119,579,016 (-)EnsemblGRCm38mm10GRCm38
MGSCv379119,392,529 - 119,488,134 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369119,332,109 - 119,427,714 (-)NCBIMGSCv36mm8
Celera9119,954,231 - 120,036,580 (-)NCBICelera
Cytogenetic Map9F3NCBI
cM Map971.33NCBI
Scn5a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542725,295,514 - 25,371,552 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542725,295,517 - 25,371,419 (+)NCBIChiLan1.0ChiLan1.0
SCN5A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1338,505,110 - 38,606,779 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0338,444,421 - 38,546,364 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1338,726,612 - 38,825,308 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl338,728,897 - 38,812,202 (-)Ensemblpanpan1.1panPan2
SCN5A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1238,278,844 - 8,374,614 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl238,280,793 - 8,358,560 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha238,320,845 - 8,398,617 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0238,569,755 - 8,663,508 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl238,567,803 - 8,663,608 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1238,383,566 - 8,461,346 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0238,524,281 - 8,602,312 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0238,517,525 - 8,595,709 (-)NCBIUU_Cfam_GSD_1.0
Scn5a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118194,744,951 - 194,825,418 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647327,883,526 - 27,963,994 (-)EnsemblSpeTri2.0
SpeTri2.0NW_00493647327,883,526 - 27,963,994 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN5A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1323,336,153 - 23,424,755 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11323,336,143 - 23,424,755 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21325,515,907 - 25,618,584 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN5A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.115767,854 - 869,787 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl15794,963 - 867,457 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660639,497,334 - 9,599,195 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn5a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247312,401,380 - 2,498,211 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247312,401,358 - 2,498,212 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn5a
498 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:884
Count of miRNA genes:249
Interacting mature miRNAs:318
Transcripts:ENSRNOT00000064555, ENSRNOT00000066932
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat
724539Cm19Cardiac mass QTL 192.6heart mass (VT:0007028)calculated heart weight (CMO:0000073)8100149864120994388Rat

Markers in Region
D8Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,320,010 - 119,320,263 (+)MAPPERmRatBN7.2
Rnor_6.08128,267,881 - 128,268,133NCBIRnor6.0
Rnor_5.08127,473,010 - 127,473,262UniSTSRnor5.0
RGSC_v3.48124,546,794 - 124,547,046UniSTSRGSC3.4
Celera8118,470,158 - 118,470,408UniSTS
Cytogenetic Map8q32UniSTS
BI294104  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,253,576 - 119,253,781 (+)MAPPERmRatBN7.2
Rnor_6.08128,202,003 - 128,202,207NCBIRnor6.0
Rnor_5.08127,408,448 - 127,408,652UniSTSRnor5.0
RGSC_v3.48124,478,999 - 124,479,203UniSTSRGSC3.4
Celera8118,404,536 - 118,404,740UniSTS
RH 3.4 Map81312.3UniSTS
Cytogenetic Map8q32UniSTS
RH94513  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.28119,221,808 - 119,221,985 (+)MAPPERmRatBN7.2
Rnor_6.08128,170,094 - 128,170,270NCBIRnor6.0
Rnor_5.08127,376,684 - 127,376,860UniSTSRnor5.0
RGSC_v3.48124,447,382 - 124,447,558UniSTSRGSC3.4
Celera8118,372,863 - 118,373,039UniSTS
RH 3.4 Map81282.5UniSTS
Cytogenetic Map8q32UniSTS
Scn3a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,432,608 - 50,433,887 (+)MAPPERmRatBN7.2
Rnor_6.0351,817,586 - 51,818,864NCBIRnor6.0
Rnor_5.0358,452,236 - 58,453,514UniSTSRnor5.0
RGSC_v3.4347,718,197 - 47,719,475UniSTSRGSC3.4
Celera350,025,799 - 50,027,077UniSTS
Cytogenetic Map7q36UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map8q32UniSTS
Cytogenetic Map3q24UniSTS


Genetic Models
This gene Scn5a is modified in the following models/strains

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 43
Low 1 4 2 4 2 1 1 60 14 10 1
Below cutoff 2 51 37 15 37 7 10 14 27 27 1 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001160162 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_013125 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006244076 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595481 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595482 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080899 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080900 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039080901 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC094738 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF353637 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ623272 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CV796639 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FM058340 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000200 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  L11243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M27902 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000064555   ⟹   ENSRNOP00000060180
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,220,905 - 119,318,769 (-)Ensembl
Rnor_6.0 Ensembl8128,169,191 - 128,266,639 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000066932   ⟹   ENSRNOP00000060586
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,220,905 - 119,318,769 (-)Ensembl
Rnor_6.0 Ensembl8128,169,191 - 128,266,639 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000082892   ⟹   ENSRNOP00000069875
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8119,220,905 - 119,318,769 (-)Ensembl
Rnor_6.0 Ensembl8128,171,379 - 128,249,538 (-)Ensembl
RefSeq Acc Id: NM_001160162   ⟹   NP_001153634
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,769 (-)NCBI
Rnor_6.08128,169,191 - 128,266,639 (-)NCBI
Rnor_5.08127,375,781 - 127,471,879 (-)NCBI
RGSC_v3.48124,446,479 - 124,545,301 (-)RGD
Celera8118,371,960 - 118,468,948 (-)RGD
Sequence:
RefSeq Acc Id: NM_013125   ⟹   NP_037257
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,769 (-)NCBI
Rnor_6.08128,169,191 - 128,266,639 (-)NCBI
Rnor_5.08127,375,781 - 127,471,879 (-)NCBI
RGSC_v3.48124,446,479 - 124,545,301 (-)RGD
Celera8118,371,960 - 118,468,948 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595481   ⟹   XP_017450970
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,815 (-)NCBI
Rnor_6.08128,169,191 - 128,266,681 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039080899   ⟹   XP_038936827
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,815 (-)NCBI
RefSeq Acc Id: XM_039080900   ⟹   XP_038936828
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,816 (-)NCBI
RefSeq Acc Id: XM_039080901   ⟹   XP_038936829
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.28119,220,905 - 119,318,815 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_037257   ⟸   NM_013125
- Peptide Label: isoform 1
- UniProtKB: Q925G6 (UniProtKB/Swiss-Prot),   P15389 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: NP_001153634   ⟸   NM_001160162
- Peptide Label: isoform 2
- UniProtKB: F1LNF5 (UniProtKB/TrEMBL),   A6I3X4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017450970   ⟸   XM_017595481
- Peptide Label: isoform X3
- UniProtKB: Q925G6 (UniProtKB/Swiss-Prot),   P15389 (UniProtKB/Swiss-Prot),   A0A0G2JWG8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069875   ⟸   ENSRNOT00000082892
RefSeq Acc Id: ENSRNOP00000060586   ⟸   ENSRNOT00000066932
RefSeq Acc Id: ENSRNOP00000060180   ⟸   ENSRNOT00000064555
RefSeq Acc Id: XP_038936828   ⟸   XM_039080900
- Peptide Label: isoform X2
- UniProtKB: Q925G6 (UniProtKB/Swiss-Prot),   P15389 (UniProtKB/Swiss-Prot),   A0A0G2JWG8 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038936827   ⟸   XM_039080899
- Peptide Label: isoform X1
- UniProtKB: Q925G6 (UniProtKB/Swiss-Prot),   P15389 (UniProtKB/Swiss-Prot),   F1LPK3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038936829   ⟸   XM_039080901
- Peptide Label: isoform X4
- UniProtKB: A6I3X4 (UniProtKB/TrEMBL)
Protein Domains
Ion transport   IQ   Sodium ion transport-associated   Voltage-gated Na+ ion channel cytoplasmic

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P15389-F1-model_v2 AlphaFold P15389 1-2019 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:3637 AgrOrtholog
BioCyc Gene G2FUF-28785 BioCyc
Ensembl Genes ENSRNOG00000015049 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000060180 ENTREZGENE
  ENSRNOP00000060180.3 UniProtKB/TrEMBL
  ENSRNOP00000060586 ENTREZGENE
  ENSRNOP00000060586.2 UniProtKB/TrEMBL
  ENSRNOP00000069875 ENTREZGENE
  ENSRNOP00000069875.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000064555 ENTREZGENE
  ENSRNOT00000064555.4 UniProtKB/TrEMBL
  ENSRNOT00000066932 ENTREZGENE
  ENSRNOT00000066932.5 UniProtKB/TrEMBL
  ENSRNOT00000082892 ENTREZGENE
  ENSRNOT00000082892.2 UniProtKB/TrEMBL
Gene3D-CATH 1.10.287.70 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  EF-hand UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  iswi atpase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_a5su UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_asu UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_chnl_inactivation_gate UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  VGCC_Ca_Na UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Volt_channel_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:25665 UniProtKB/Swiss-Prot
NCBI Gene 25665 ENTREZGENE
PANTHER PTHR10037 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SODIUM CHANNEL PROTEIN TYPE 5 SUBUNIT ALPHA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Ion_trans UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_assoc UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_trans_cytopl UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB SCN5A RGD
PhenoGen Scn5a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NACHANNEL5 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Voltage-gated potassium channels UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2JWG8 ENTREZGENE, UniProtKB/TrEMBL
  A4ZYR8_RAT UniProtKB/TrEMBL
  A6I3X4 ENTREZGENE, UniProtKB/TrEMBL
  F1LNF5 ENTREZGENE, UniProtKB/TrEMBL
  F1LPK3 ENTREZGENE, UniProtKB/TrEMBL
  P15389 ENTREZGENE
  Q6EWG5_RAT UniProtKB/TrEMBL
  Q925G6 ENTREZGENE
  SCN5A_RAT UniProtKB/Swiss-Prot
UniProt Secondary Q925G6 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-11 Scn5a  sodium voltage-gated channel alpha subunit 5  Scn5a  sodium channel, voltage-gated, type V, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-09-16 Scn5a  sodium channel, voltage-gated, type V, alpha subunit  Scn5a  sodium channel, voltage-gated, type V, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-12-15 Scn5a  sodium channel, voltage-gated, type V, alpha  Scn5a  sodium channel, voltage-gated, type V, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2009-05-18 Scn5a  sodium channel, voltage-gated, type V, alpha subunit  Scn5a  sodium channel, voltage-gated, type 5, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-15 Scn5a  sodium channel, voltage-gated, type 5, alpha subunit  Scn5a  sodium channel, voltage-gated, type V, alpha polypeptide  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Scn5a  Sodium channel, voltage-gated, type V, alpha polypeptide      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutation of the human homolog cause Brugada syndrome, a cardiac disorder that leads to ventricular fibrillation and sudden death 735235