Scn1a (sodium voltage-gated channel alpha subunit 1) - Rat Genome Database

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Gene: Scn1a (sodium voltage-gated channel alpha subunit 1) Rattus norvegicus
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Symbol: Scn1a
Name: sodium voltage-gated channel alpha subunit 1
RGD ID: 69364
Description: Enables sodium ion binding activity and voltage-gated sodium channel activity. Involved in neuronal action potential. Located in plasma membrane. Part of voltage-gated sodium channel complex. Is integral component of presynaptic membrane. Human ortholog(s) of this gene implicated in Dravet syndrome; developmental and epileptic encephalopathy; familial hemiplegic migraine 3; generalized epilepsy with febrile seizures plus; and generalized epilepsy with febrile seizures plus 2. Orthologous to human SCN1A (sodium voltage-gated channel alpha subunit 1); INTERACTS WITH 1-bromopropane; 1-naphthyl isothiocyanate; 2,2',4,4'-Tetrabromodiphenyl ether.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC102553713; sodium channel protein brain I subunit alpha; sodium channel protein type 1 subunit alpha; sodium channel protein type 1 subunit alpha-like; sodium channel protein type I subunit alpha; sodium channel protein, brain I subunit alpha; sodium channel voltage-gated type I alpha polypeptide; sodium channel, voltage-gated, type 1, alpha polypeptide; sodium channel, voltage-gated, type I, alpha; sodium channel, voltage-gated, type I, alpha polypeptide; sodium channel, voltage-gated, type I, alpha subunit; voltage-gated sodium channel subunit alpha Nav1.1
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: Scn1am1Kyo   Scn1am2Kyo  
Genetic Models: F344-Scn1am1Kyo F344-Scn1am2Kyo
Is Marker For: Strains:   F344.NER-(D1Mgh6-D1Rat73)(D5Mgh4-D5Rat36)Scn1am1/Kyo  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)Ensembl
Rnor_6.0352,388,811 - 52,533,365 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,381,975 - 52,510,507 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0359,016,641 - 59,135,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4348,238,528 - 48,364,143 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1348,134,899 - 48,260,515 (-)NCBI
Celera350,540,798 - 50,655,298 (-)NCBICelera
Cytogenetic Map3q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
absence epilepsy  (ISO)
autism spectrum disorder  (ISO)
autistic disorder  (ISO)
autosomal dominant nocturnal frontal lobe epilepsy  (ISO)
benign epilepsy with centrotemporal spikes  (ISO)
Benign Familial Infantile Seizures, 3  (ISO)
developmental and epileptic encephalopathy  (ISO)
developmental and epileptic encephalopathy 1  (ISO)
developmental and epileptic encephalopathy 11  (ISO)
Developmental and Epileptic Encephalopathy 6B  (ISO)
Developmental Disabilities  (ISO)
Dravet syndrome  (ISO)
early infantile epileptic encephalopathy  (ISO)
early myoclonic encephalopathy  (ISO)
epilepsy  (ISO)
familial febrile seizures 1  (ISO)
Familial Febrile Seizures 3A  (ISO)
familial hemiplegic migraine  (ISO)
familial hemiplegic migraine 3  (ISO)
Febrile Seizures  (IMP,ISO)
focal epilepsy  (ISO)
Generalized Epilepsy  (ISO)
generalized epilepsy with febrile seizures plus  (ISO,ISS)
generalized epilepsy with febrile seizures plus 1  (ISO)
generalized epilepsy with febrile seizures plus 2  (ISO)
generalized epilepsy with febrile seizures plus 7  (ISO)
genetic disease  (ISO)
hereditary sensory and autonomic neuropathy type 2A  (ISO)
hereditary sensory neuropathy  (ISO)
hereditary spastic paraplegia 11  (ISO)
Hip Contracture  (ISO)
Hypertelorism  (ISO)
intellectual disability  (ISO)
Lennox-Gastaut syndrome  (ISO)
microcephaly  (ISO)
movement disease  (ISO)
Myoclonic Epilepsies  (ISO)
Nervous System Malformations  (ISO)
Neurodevelopmental Disorders  (ISO)
Plagiocephaly  (ISO)
sudden infant death syndrome  (ISO)
syringomyelia  (ISO)
visual epilepsy  (ISO)
West syndrome  (ISO)

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

Additional References at PubMed
PMID:1658739   PMID:10769382   PMID:10827969   PMID:12835125   PMID:15272007   PMID:15746173   PMID:15797713   PMID:15878599   PMID:16921370   PMID:16966585   PMID:17228331   PMID:17322896  
PMID:17537961   PMID:17709186   PMID:17884088   PMID:17928448   PMID:19426735   PMID:19765660   PMID:20483028   PMID:20707984   PMID:20875856   PMID:21714116   PMID:22871113   PMID:22920678  
PMID:22992729   PMID:23219908   PMID:23318929   PMID:23375560   PMID:26259688   PMID:26528804   PMID:26978272   PMID:27207958   PMID:27281198   PMID:29956586   PMID:32318899   PMID:32377688  
PMID:33045260  


Genomics

Candidate Gene Status
Scn1a is a candidate Gene for QTL Alc19
Comparative Map Data
Scn1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)Ensembl
Rnor_6.0352,388,811 - 52,533,365 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl352,381,975 - 52,510,507 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0359,016,641 - 59,135,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4348,238,528 - 48,364,143 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1348,134,899 - 48,260,515 (-)NCBI
Celera350,540,798 - 50,655,298 (-)NCBICelera
Cytogenetic Map3q21NCBI
SCN1A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2165,984,641 - 166,149,214 (-)EnsemblGRCh38hg38GRCh38
GRCh382165,984,641 - 166,149,161 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372166,841,151 - 167,005,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362166,553,916 - 166,638,395 (-)NCBINCBI36hg18NCBI36
Build 342166,673,232 - 166,755,638NCBI
Celera2160,455,660 - 160,540,161 (-)NCBI
Cytogenetic Map2q24.3NCBI
HuRef2158,727,062 - 158,886,965 (-)NCBIHuRef
CHM1_12166,851,977 - 167,011,835 (-)NCBICHM1_1
Scn1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39266,101,125 - 66,271,181 (-)NCBIGRCm39mm39
GRCm39 Ensembl266,101,122 - 66,271,184 (-)Ensembl
GRCm38266,270,781 - 66,440,837 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl266,270,778 - 66,440,840 (-)EnsemblGRCm38mm10GRCm38
MGSCv37266,108,839 - 66,278,894 (-)NCBIGRCm37mm9NCBIm37
MGSCv36266,071,621 - 66,241,676 (-)NCBImm8
Celera267,950,131 - 68,119,920 (-)NCBICelera
Cytogenetic Map2C1.3NCBI
cM Map239.13NCBI
Scn1a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554498,160,986 - 8,221,951 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554498,072,910 - 8,220,763 (+)NCBIChiLan1.0ChiLan1.0
SCN1A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12B170,736,651 - 170,826,069 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2B170,736,651 - 170,822,014 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02B53,258,614 - 53,348,131 (-)NCBIMhudiblu_PPA_v0panPan3
SCN1A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13611,105,936 - 11,245,978 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3611,108,050 - 11,183,496 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3611,250,750 - 11,390,861 (-)NCBI
ROS_Cfam_1.03611,240,396 - 11,380,203 (-)NCBI
ROS_Cfam_1.0 Ensembl3611,240,401 - 11,380,345 (-)Ensembl
UMICH_Zoey_3.13611,322,130 - 11,462,589 (-)NCBI
UNSW_CanFamBas_1.03611,294,554 - 11,434,591 (-)NCBI
UU_Cfam_GSD_1.03611,407,225 - 11,547,338 (-)NCBI
Scn1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303128,271,735 - 128,421,841 (-)NCBI
SpeTri2.0NW_00493646913,194,769 - 13,345,979 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCN1A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1572,529,875 - 72,678,067 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11572,529,866 - 72,696,715 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21581,177,412 - 81,188,630 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCN1A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11051,490,204 - 51,653,916 (-)NCBIChlSab1.1chlSab2
ChlSab1.11051,490,204 - 51,653,916 (-)NCBIChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040147,883,083 - 148,032,547 (+)NCBIVero_WHO_p1.0
Scn1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247873,767,405 - 3,939,065 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
D3Rat181  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,968,507 - 50,968,636 (+)MAPPERmRatBN7.2
Rnor_6.0352,408,191 - 52,408,319NCBIRnor6.0
Rnor_5.0359,034,932 - 59,035,060UniSTSRnor5.0
RGSC_v3.4348,254,474 - 48,254,603RGDRGSC3.4
RGSC_v3.4348,254,475 - 48,254,603UniSTSRGSC3.4
RGSC_v3.1348,150,760 - 48,150,995RGD
Celera350,556,511 - 50,556,639UniSTS
SHRSP x BN Map336.0899UniSTS
SHRSP x BN Map336.0899RGD
Cytogenetic Map3q21UniSTS
SCN1A_3451  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,954,797 - 50,955,708 (+)MAPPERmRatBN7.2
Rnor_6.0352,383,990 - 52,384,900NCBIRnor6.0
Rnor_6.0352,390,819 - 52,391,729NCBIRnor6.0
Rnor_5.0359,018,648 - 59,019,558UniSTSRnor5.0
Rnor_5.0359,011,819 - 59,012,729UniSTSRnor5.0
RGSC_v3.4348,240,535 - 48,241,445UniSTSRGSC3.4
Celera350,542,805 - 50,543,715UniSTS
Cytogenetic Map3q21UniSTS
Scn1a  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2350,432,608 - 50,433,910 (+)MAPPERmRatBN7.2
Rnor_6.0351,817,586 - 51,818,887NCBIRnor6.0
Rnor_5.0358,452,236 - 58,453,537UniSTSRnor5.0
RGSC_v3.4347,718,197 - 47,719,498UniSTSRGSC3.4
Celera350,025,799 - 50,027,100UniSTS
Cytogenetic Map3q21UniSTS
Cytogenetic Map3q24UniSTS
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 Map3q24UniSTS
Cytogenetic Map8q32UniSTS
Cytogenetic Map3q21UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3