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
Analyze
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 active in 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
Previously 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  
Candidate Gene For: Alc19
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx354,295,423 - 54,414,933 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0362,879,049 - 62,998,545 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0360,659,682 - 60,779,082 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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)
asphyxiating thoracic dystrophy  (ISO)
asphyxiating thoracic dystrophy 1  (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)
benign familial neonatal epilepsy  (ISO)
childhood onset epileptic encephalopathy  (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)
epilepsy with generalized tonic-clonic seizures  (ISO)
familial febrile seizures 1  (ISO)
Familial Febrile Seizures 3A  (ISO)
familial hemiplegic migraine  (ISO)
familial hemiplegic migraine 3  (ISO)
Familial Sudden Death  (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)
Muscle Hypotonia  (ISO)
Myoclonic Epilepsies  (ISO)
nephronophthisis  (ISO)
nephronophthisis 1  (ISO)
Nervous System Malformations  (ISO)
Neurodevelopmental Disorders  (ISO)
Plagiocephaly  (ISO)
sudden infant death syndrome  (ISO)
Vision Disorders  (ISO)
visual epilepsy  (ISO)
West syndrome  (ISO)

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

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Downregulation of neuronal sodium channel subunits Nav1.1 and Nav1.6 in the sinoatrial node from volume-overloaded heart failure rat. Du Y, etal., Pflugers Arch. 2007 Jun;454(3):451-9. Epub 2007 Feb 2.
2. Mutations of SCN1A, encoding a neuronal sodium channel, in two families with GEFS+2. Escayg A, etal., Nat Genet 2000 Apr;24(4):343-5.
3. 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.
4. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
5. Autosomal dominant epilepsy with febrile seizures plus with missense mutations of the (Na+)-channel alpha 1 subunit gene, SCN1A. Ito M, etal., Epilepsy Res 2002 Jan;48(1-2):15-23.
6. A missense mutation of the gene encoding voltage-dependent sodium channel (Nav1.1) confers susceptibility to febrile seizures in rats. Mashimo T, etal., J Neurosci. 2010 Apr 21;30(16):5744-53. doi: 10.1523/JNEUROSCI.3360-09.2010.
7. Molecular diversity of voltage-gated sodium channel alpha subunits expressed in neuronal and non-neuronal excitable cells. Mechaly I, etal., Neuroscience. 2005;130(2):389-96.
8. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
9. Voltage-gated sodium channel alpha-subunits Na(v)1.1, Na(v)1.2, and Na(v)1.6 in the distal mammalian retina. Mojumder DK, etal., Mol Vis. 2007 Nov 27;13:2163-82.
10. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
11. Structure and function of sodium channel. Noda M and Numa S, J Recept Res 1987;7(1-4):467-97.
12. Existence of distinct sodium channel messenger RNAs in rat brain. Noda M, etal., Nature 1986 Mar 13-19;320(6058):188-92.
13. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
14. Sodium currents in medullary neurons isolated from the pre-Botzinger complex region. Ptak K, etal., J Neurosci. 2005 May 25;25(21):5159-70.
15. GOA pipeline RGD automated data pipeline
16. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
17. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
18. Tentative Sequence Identification Numbers Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
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

Comparative Map Data
Scn1a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2350,952,790 - 51,071,804 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx354,295,423 - 54,414,933 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0362,879,049 - 62,998,545 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0360,659,682 - 60,779,082 (-)NCBIRnor_WKY
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 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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
GRCh382165,984,641 - 166,149,161 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl2165,984,641 - 166,149,214 (-)EnsemblGRCh38hg38GRCh38
GRCh372166,841,151 - 167,005,671 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362166,553,916 - 166,638,395 (-)NCBINCBI36Build 36hg18NCBI36
Build 342166,673,232 - 166,755,638NCBI
Celera2160,455,660 - 160,540,161 (-)NCBICelera
Cytogenetic Map2q24.3NCBI
HuRef2158,727,062 - 158,886,965 (-)NCBIHuRef
CHM1_12166,851,977 - 167,011,835 (-)NCBICHM1_1
T2T-CHM13v2.02166,442,174 - 166,606,734 (-)NCBIT2T-CHM13v2.0
Scn1a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39266,101,125 - 66,271,181 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl266,101,122 - 66,271,184 (-)EnsemblGRCm39 Ensembl
GRCm38266,270,781 - 66,440,837 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl266,270,778 - 66,440,840 (-)EnsemblGRCm38mm10GRCm38
MGSCv37266,108,839 - 66,278,894 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36266,071,621 - 66,241,676 (-)NCBIMGSCv36mm8
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_v0Mhudiblu_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 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.03611,240,396 - 11,380,203 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl3611,240,401 - 11,380,345 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.13611,322,130 - 11,462,589 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.03611,294,554 - 11,434,591 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.03611,407,225 - 11,547,338 (-)NCBIUU_Cfam_GSD_1.0
Scn1a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405303128,271,735 - 128,421,841 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493646913,256,925 - 13,345,978 (+)EnsemblSpeTri2.0
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 - 72,678,066 (-)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 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666040147,883,083 - 148,032,547 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scn1a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247873,768,120 - 3,908,889 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247873,767,405 - 3,939,065 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scn1a
917 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:99
Count of miRNA genes:71
Interacting mature miRNAs:89
Transcripts:ENSRNOT00000008026
Prediction methods:Miranda, 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
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)314489145121056321Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)314489145121056321Rat
2298542Neuinf11Neuroinflammation QTL 113.9nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)31500542276927699Rat
631676Cm8Cardiac mass QTL 87.030.0001aorta mass (VT:0002845)aorta weight (CMO:0000076)31695470861954708Rat
10450804Scl70Serum cholesterol level QTL 704.70.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
10450794Scl69Serum cholesterol level QTL 696.30.001blood LDL cholesterol amount (VT:0000181)blood low density lipoprotein cholesterol level (CMO:0000053)32071409065714090Rat
2302055Pia30Pristane induced arthritis QTL 303.50.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)32793691972936919Rat
9590286Uminl1Urine mineral level QTL 13.50.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)32824968773249687Rat
8694196Abfw2Abdominal fat weight QTL 216.580.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)32824968773249687Rat
8694386Bw159Body weight QTL 1594.520.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)32824968773249687Rat
8552950Pigfal12Plasma insulin-like growth factor 1 level QTL 127.3blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)32824968773249687Rat
9590136Scort3Serum corticosterone level QTL 323.370.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)32824968773249687Rat
2303593Gluco46Glucose level QTL 463blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)32846857173468571Rat
1354590Despr11Despair related QTL 110.000031locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)32846857173468571Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)329463235118376539Rat
61419Cia11Collagen induced arthritis QTL 115.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)33035677398535386Rat
61356Bp37Blood pressure QTL 373blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)33068464275684642Rat
631647Bp122Blood pressure QTL 1226.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)33068464275684642Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)331172320163586636Rat
11565451Bw177Body weight QTL 1770.002body mass (VT:0001259)body weight (CMO:0000012)33142640370668733Rat
11565452Kidm57Kidney mass QTL 570.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)33142640370668733Rat
12879866Cm94Cardiac mass QTL 940.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)33142640370668733Rat
12879867Cm95Cardiac mass QTL 950.047heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)33142640370668733Rat
12879868Am6Aortic mass QTL 60.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)33142640370668733Rat
2301400Cm68Cardiac mass QTL 680.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)33142640370668733Rat
1300169Bp177Blood pressure QTL 1772.96arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)33370334761017857Rat
1354589Bw31Body weight QTL 313.3body mass (VT:0001259)body weight (CMO:0000012)33370334778196190Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)333703347104104347Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)338192233133483320Rat
738019Anxrr10Anxiety related response QTL 103.9exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)33851780383517803Rat
634317Bw117Body weight QTL 1173.58abdominal fat pad mass (VT:1000711)abdominal fat pad weight to body weight ratio (CMO:0000095)33945463753296578Rat
2302276Bw82Body weight QTL 824.32body mass (VT:0001259)body weight (CMO:0000012)33945463762951183Rat
1331777Bw24Body weight QTL 243.503body mass (VT:0001259)body weight (CMO:0000012)33945463789115240Rat
1331795Rf30Renal function QTL 303.708urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)33945463789115240Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)341874578104104347Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)341874578155617519Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)341874578155617519Rat
1300178Hrtrt4Heart rate QTL 43.74heart pumping trait (VT:2000009)heart rate (CMO:0000002)34382736490905114Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)343827364121056321Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)343827364169034231Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)347233211147415807Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)347233430110362260Rat
631665Bw8Body weight QTL 85.5body mass (VT:0001259)body weight (CMO:0000012)350437042119183768Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)350437504115638231Rat

Markers in Region
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_6.0352,390,819 - 52,391,729NCBIRnor6.0
Rnor_6.0352,383,990 - 52,384,900NCBIRnor6.0
Rnor_5.0359,011,819 - 59,012,729UniSTSRnor5.0
Rnor_5.0359,018,648 - 59,019,558UniSTSRnor5.0
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 Map3q21UniSTS
Cytogenetic Map8q32UniSTS
Cytogenetic Map3q24UniSTS


Related Rat Strains
The following Strains have been annotated to Scn1a


Genetic Models
This gene Scn1a 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

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 25
Low 26 8 8 47 7 8
Below cutoff 15 18 5 12 5 1 2 29 29 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_030875 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761923 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761924 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008761925 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592055 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592056 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592057 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105911 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105913 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105914 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105915 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_001837049 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501990 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005501991 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AC122968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  FQ212107 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000115 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  M22253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X03638 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000079020   ⟹   ENSRNOP00000068852
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,954,907 - 51,071,699 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083552   ⟹   ENSRNOP00000074819
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,954,642 - 51,071,699 (-)Ensembl
Rnor_6.0 Ensembl352,381,975 - 52,447,622 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000091259   ⟹   ENSRNOP00000073986
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl350,952,791 - 51,071,699 (-)Ensembl
Rnor_6.0 Ensembl352,388,812 - 52,510,507 (-)Ensembl
RefSeq Acc Id: NM_030875   ⟹   NP_110502
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,791 - 51,071,699 (-)NCBI
Rnor_6.0352,388,812 - 52,510,507 (-)NCBI
Rnor_5.0359,016,641 - 59,135,580 (-)NCBI
RGSC_v3.4348,238,528 - 48,364,143 (-)RGD
Celera350,540,798 - 50,655,298 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105911   ⟹   XP_038961839
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,790 - 51,071,793 (-)NCBI
RefSeq Acc Id: XM_039105912   ⟹   XP_038961840
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,790 - 51,071,796 (-)NCBI
RefSeq Acc Id: XM_039105913   ⟹   XP_038961841
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,790 - 51,071,795 (-)NCBI
RefSeq Acc Id: XM_039105914   ⟹   XP_038961842
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,974,073 - 51,071,804 (-)NCBI
RefSeq Acc Id: XM_039105915   ⟹   XP_038961843
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,790 - 50,997,446 (-)NCBI
RefSeq Acc Id: XR_005501990
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,952,790 - 51,071,795 (-)NCBI
RefSeq Acc Id: XR_005501991
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2350,965,225 - 51,071,804 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_110502   ⟸   NM_030875
- UniProtKB: A0A0G2K6Y2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073986   ⟸   ENSRNOT00000091259
RefSeq Acc Id: ENSRNOP00000074819   ⟸   ENSRNOT00000083552
RefSeq Acc Id: XP_038961840   ⟸   XM_039105912
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038961841   ⟸   XM_039105913
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038961839   ⟸   XM_039105911
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038961843   ⟸   XM_039105915
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038961842   ⟸   XM_039105914
- Peptide Label: isoform X4
RefSeq Acc Id: ENSRNOP00000068852   ⟸   ENSRNOT00000079020
Protein Domains
Ion_trans   IQ   Na_trans_assoc   Na_trans_cytopl

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P04774-F1-model_v2 AlphaFold P04774 1-2009 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:69364 AgrOrtholog
BioCyc Gene G2FUF-49546 BioCyc
Ensembl Genes ENSRNOG00000053122 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000068852.2 UniProtKB/TrEMBL
  ENSRNOP00000073986 ENTREZGENE
  ENSRNOP00000073986.1 UniProtKB/TrEMBL
  ENSRNOP00000074819 ENTREZGENE
  ENSRNOP00000074819.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000079020.2 UniProtKB/TrEMBL
  ENSRNOT00000083552 ENTREZGENE
  ENSRNOT00000083552.2 UniProtKB/TrEMBL
  ENSRNOT00000091259 ENTREZGENE
  ENSRNOT00000091259.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.120.350 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Ion_trans_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Na_channel_a1su 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:81574 UniProtKB/Swiss-Prot
NCBI Gene 81574 ENTREZGENE
PANTHER PTHR10037 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 SCN1A RGD
PhenoGen Scn1a PhenoGen
PRINTS NACHANNEL UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  NACHANNEL1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC235885
UniProt A0A0G2K6Y2 ENTREZGENE, UniProtKB/TrEMBL
  A0A0G2K914_RAT UniProtKB/TrEMBL
  A0A8L2R0Q2_RAT UniProtKB/TrEMBL
  P04774 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Scn1a  sodium voltage-gated channel alpha subunit 1  LOC102553713  sodium channel protein type 1 subunit alpha-like  Data Merged 737654 PROVISIONAL
2016-02-11 Scn1a  sodium voltage-gated channel alpha subunit 1  Scn1a  sodium channel, voltage-gated, type I, alpha subunit  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-03-13 Scn1a  sodium channel, voltage-gated, type I, alpha subunit  Scn1a  sodium channel, voltage-gated, type I, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-12-17 LOC102553713  sodium channel protein type 1 subunit alpha-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-03-30 Scn1a  sodium channel, voltage-gated, type I, alpha    sodium channel, voltage-gated, type 1, alpha polypeptide  Name updated 1299863 APPROVED
2002-06-10 Scn1a  sodium channel, voltage-gated, type 1, alpha polypeptide      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_disease mutations of the human homolog are detected in generalized epilepsy with febrile seizures plus (GEFS+) 727292